351
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Xie S, Syrenne R, Sun S, Yuan JS. Exploration of Natural Biomass Utilization Systems (NBUS) for advanced biofuel--from systems biology to synthetic design. Curr Opin Biotechnol 2014; 27:195-203. [PMID: 24657913 DOI: 10.1016/j.copbio.2014.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 12/24/2022]
Abstract
Efficient degradation and utilization of lignocellulosic biomass remains a challenge for sustainable and affordable biofuels. Various natural biomass utilization systems (NBUS) evolved the capacity to combat the recalcitrance of plant cell walls. The study of these NBUS could enable the development of efficient and cost-effective biocatalysts, microorganisms, and bioprocesses for biofuels and bioproducts. Here, we reviewed the recent research progresses for several NBUS, ranging from single cell microorganisms to consortiums such as cattle rumen and insect guts. These studies aided the discovery of biomass-degrading enzymes and the elucidation of the evolutionary and functional relevance in these systems. In particular, advances in the next generation 'omics' technologies offered new opportunities to explore NBUS in a high-throughput manner. Systems biology helped to facilitate the rapid biocatalyst discovery and detailed mechanism analysis, which could in turn guide the reverse design of engineered microorganisms and bioprocesses for cost-effective and efficient biomass conversion.
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Affiliation(s)
- Shangxian Xie
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States
| | - Ryan Syrenne
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States; Molecular & Environmental Plant Sciences, Texas A&M University, College Station, TX 77843, United States
| | - Su Sun
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States
| | - Joshua S Yuan
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States.
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352
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Lapkin A, Adou E, Mlambo BN, Chemat S, Suberu J, Collis AE, Clark A, Barker G. Integrating medicinal plants extraction into a high-value biorefinery: An example of Artemisia annua L. CR CHIM 2014. [DOI: 10.1016/j.crci.2013.10.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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353
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Gall DL, Kim H, Lu F, Donohue TJ, Noguera DR, Ralph J. Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway. J Biol Chem 2014; 289:8656-67. [PMID: 24509858 PMCID: PMC3961688 DOI: 10.1074/jbc.m113.536250] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Glutathione-dependent enzymes play important protective, repair, or metabolic roles in cells. In particular, enzymes in the glutathione S-transferase (GST) superfamily function in stress responses, defense systems, or xenobiotic detoxification. Here, we identify novel features of bacterial GSTs that cleave β-aryl ether bonds typically found in plant lignin. Our data reveal several original features of the reaction cycle of these GSTs, including stereospecific substrate recognition and stereoselective formation of β-S-thioether linkages. Products of recombinant GSTs (LigE, LigP, and LigF) are β-S-glutathionyl-α-keto-thioethers that are degraded by a β-S-thioetherase (LigG). All three Lig GSTs produced the ketone product (β-S-glutathionyl-α-veratrylethanone) from an achiral side chain-truncated model substrate (β-guaiacyl-α-veratrylethanone). However, when β-etherase assays were conducted with a racemic model substrate, β-guaiacyl-α-veratrylglycerone, LigE- or LigP-catalyzed reactions yielded only one of two potential product (β-S-glutathionyl-α-veratrylglycerone) epimers, whereas the other diastereomer (differing in configuration at the β-position (i.e. its β-epimer)) was produced only in the LigF-catalyzed reaction. Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF). Further, LigG catalyzed glutathione-dependent β-S-thioether cleavage with β-S-glutathionyl-α-veratrylethanone and with β(R)-configured β-S-glutathionyl-α-veratrylglycerone but exhibited no or significantly reduced β-S-thioether-cleaving activity with the β(S)-epimer, demonstrating that LigG is a stereospecific β-thioetherase. We therefore propose that multiple Lig enzymes are needed in this β-aryl etherase pathway in order to cleave the racemic β-ether linkages that are present in the backbone of the lignin polymer.
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Affiliation(s)
- Daniel L Gall
- From the Departments of Civil and Environmental Engineering
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354
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Paliwal V, Raju SC, Modak A, Phale PS, Purohit HJ. Pseudomonas putida CSV86: a candidate genome for genetic bioaugmentation. PLoS One 2014; 9:e84000. [PMID: 24475028 PMCID: PMC3901652 DOI: 10.1371/journal.pone.0084000] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 11/11/2013] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas putida CSV86, a plasmid-free strain possessing capability to transfer the naphthalene degradation property, has been explored for its metabolic diversity through genome sequencing. The analysis of draft genome sequence of CSV86 (6.4 Mb) revealed the presence of genes involved in the degradation of naphthalene, salicylate, benzoate, benzylalcohol, p-hydroxybenzoate, phenylacetate and p-hydroxyphenylacetate on the chromosome thus ensuring the stability of the catabolic potential. Moreover, genes involved in the metabolism of phenylpropanoid and homogentisate, as well as heavy metal resistance, were additionally identified. Ability to grow on vanillin, veratraldehyde and ferulic acid, detection of inducible homogentisate dioxygenase and growth on aromatic compounds in the presence of heavy metals like copper, cadmium, cobalt and arsenic confirm in silico observations reflecting the metabolic versatility. In silico analysis revealed the arrangement of genes in the order: tRNAGly, integrase followed by nah operon, supporting earlier hypothesis of existence of a genomic island (GI) for naphthalene degradation. Deciphering the genomic architecture of CSV86 for aromatic degradation pathways and identification of elements responsible for horizontal gene transfer (HGT) suggests that genetic bioaugmentation strategies could be planned using CSV86 for effective bioremediation.
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Affiliation(s)
- Vasundhara Paliwal
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Sajan C Raju
- MEM-Group, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Arnab Modak
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, India
| | - Hemant J Purohit
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
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355
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Hara S, Desyatkin R, Hashidoko Y. Investigation of the mechanisms underlying the high acetylene-reducing activity exhibited by the soil bacterial community from BC2 horizon in the permafrost zone of the East Siberian larch forest bed. J Appl Microbiol 2014; 116:865-76. [DOI: 10.1111/jam.12424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 12/02/2013] [Accepted: 12/09/2013] [Indexed: 11/27/2022]
Affiliation(s)
- S. Hara
- Graduate School and Research Faculty of Agriculture; Hokkaido University; Sapporo Hokkaido Japan
| | - R.V. Desyatkin
- Institute of Biological Problems of Cryolithzone; Russian Academy of Sciences; Yakutsk Russia
| | - Y. Hashidoko
- Graduate School and Research Faculty of Agriculture; Hokkaido University; Sapporo Hokkaido Japan
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356
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Fernandes TAR, Silveira WBD, Passos FML, Zucchi TD. Laccases from <i>Actinobacteria</i>—What We Have and What to Expect. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/aim.2014.46035] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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358
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Kurtböke DI, French JRJ, Hayes RA, Quinn RJ. Eco-taxonomic insights into actinomycete symbionts of termites for discovery of novel bioactive compounds. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 147:111-35. [PMID: 24817085 DOI: 10.1007/10_2014_270] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Termites play a major role in foraging and degradation of plant biomass as well as cultivating bioactive microorganisms for their defense. Current advances in "omics" sciences are revealing insights into function-related presence of these symbionts, and their related biosynthetic activities and genes identified in gut symbiotic bacteria might offer a significant potential for biotechnology and biodiscovery. Actinomycetes have been the major producers of bioactive compounds with an extraordinary range of biological activities. These metabolites have been in use as anticancer agents, immune suppressants, and most notably, as antibiotics. Insect-associated actinomycetes have also been reported to produce a range of antibiotics such as dentigerumycin and mycangimycin. Advances in genomics targeting a single species of the unculturable microbial members are currently aiding an improved understanding of the symbiotic interrelationships among the gut microorganisms as well as revealing the taxonomical identity and functions of the complex multilayered symbiotic actinofloral layers. If combined with target-directed approaches, these molecular advances can provide guidance towards the design of highly selective culturing methods to generate further information related to the physiology and growth requirements of these bioactive actinomycetes associated with the termite guts. This chapter provides an overview on the termite gut symbiotic actinoflora in the light of current advances in the "omics" science, with examples of their detection and selective isolation from the guts of the Sunshine Coast regional termite Coptotermes lacteus in Queensland, Australia.
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Affiliation(s)
- D Ipek Kurtböke
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia,
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359
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Colpa DI, Fraaije MW, van Bloois E. DyP-type peroxidases: a promising and versatile class of enzymes. ACTA ACUST UNITED AC 2014; 41:1-7. [DOI: 10.1007/s10295-013-1371-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 10/17/2013] [Indexed: 10/26/2022]
Abstract
Abstract
DyP peroxidases comprise a novel superfamily of heme-containing peroxidases, which is unrelated to the superfamilies of plant and animal peroxidases. These enzymes have so far been identified in the genomes of fungi, bacteria, as well as archaea, although their physiological function is still unclear. DyPs are bifunctional enzymes displaying not only oxidative activity but also hydrolytic activity. Moreover, these enzymes are able to oxidize a variety of organic compounds of which some are poorly converted by established peroxidases, including dyes, β-carotene, and aromatic sulfides. Interestingly, accumulating evidence shows that microbial DyP peroxidases play a key role in the degradation of lignin. Owing to their unique properties, these enzymes are potentially interesting for a variety of biocatalytic applications. In this review, we deal with the biochemical and structural features of DyP-type peroxidases as well as their promising biotechnological potential.
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Affiliation(s)
- Dana I Colpa
- grid.4830.f 0000000404071981 Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Marco W Fraaije
- grid.4830.f 0000000404071981 Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Edwin van Bloois
- grid.4830.f 0000000404071981 Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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360
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Fernández-Fueyo E, Ruiz-Dueñas FJ, Martínez AT. Engineering a fungal peroxidase that degrades lignin at very acidic pH. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:114. [PMID: 25788979 PMCID: PMC4364632 DOI: 10.1186/1754-6834-7-114] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/15/2014] [Indexed: 05/17/2023]
Abstract
BACKGROUND Ligninolytic peroxidases are divided into three families: manganese peroxidases (MnPs), lignin peroxidases (LiPs), and versatile peroxidases (VPs). The latter two are able to degrade intact lignins, as shown using nonphenolic lignin model compounds, with VP oxidizing the widest range of recalcitrant substrates. One of the main limiting issues for the use of these two enzymes in lignocellulose biorefineries (for delignification and production of cellulose-based products or modification of industrial lignins to added-value products) is their progressive inactivation under acidic pH conditions, where they exhibit the highest oxidative activities. RESULTS In the screening of peroxidases from basidiomycete genomes, one MnP from Ceriporiopsis subvermispora was found to have a remarkable acidic stability. The crystal structure of this enzyme recently became available and, after comparison with Pleurotus ostreatus VP and Phanerochaete chrysosporium LiP structures, it was used as a robust scaffold to engineer a stable VP by introducing an exposed catalytic tryptophan, with different protein environments. The variants obtained largely maintain the acidic stability and strong Mn(2+)-oxidizing activity of the parent enzyme, and the ability to oxidize veratryl alcohol and Reactive Black 5 (two simple VP substrates) was introduced. The engineered peroxidases present more acidic optimal pH than the best VP from P. ostreatus, enabling higher catalytic efficiency oxidizing lignins, by lowering the reaction pH, as shown using a nonphenolic model dimer. CONCLUSIONS A peroxidase that degrades lignin at very acidic pH could be obtained by engineering an exposed catalytic site, able to oxidize the bulky and recalcitrant lignin polymers, in a different peroxidase type selected because of its high stability at acidic pH. The potential of this type of engineered peroxidases as industrial biocatalysts in lignocellulose biorefineries is strongly enhanced by the possibility to perform the delignification (or lignin modification) reactions under extremely acidic pH conditions (below pH 2), resulting in enhanced oxidative power of the enzymes.
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Affiliation(s)
- Elena Fernández-Fueyo
- />Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
- />Department of Biotechnology, TU Delft, Julianalaan 136, 2628 BL Delft, Netherlands
| | | | - Angel T Martínez
- />Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
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361
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Fernandes TAR, da Silveira WB, Passos FML, Zucchi TD. Characterization of a thermotolerant laccase produced by Streptomyces sp. SB086. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0781-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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362
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Hervé V, Le Roux X, Uroz S, Gelhaye E, Frey-Klett P. Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay. Environ Microbiol 2013; 16:2238-52. [PMID: 24286477 DOI: 10.1111/1462-2920.12347] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/23/2013] [Indexed: 01/05/2023]
Abstract
Wood recycling is key to forest biogeochemical cycles, largely driven by microorganisms such as white-rot fungi which naturally coexist with bacteria in the environment. We have tested whether and to what extent the diversity of the bacterial community associated with wood decay is determined by wood and/or by white-rot fungus Phanerochaete chrysosporium. We combined a microcosm approach with an enrichment procedure, using beech sawdust inoculated with or without P.chrysosporium. During 18 weeks, we used 16S rRNA gene-based pyrosequencing to monitor the forest bacterial community inoculated into these microcosms. We found bacterial communities associated with wood to be substantially less diverse than the initial forest soil inoculum. The presence of most bacterial operational taxonomic units (OTUs) varied over time and between replicates, regardless of their treatment, suggestive of the stochastic processes. However, we observed two OTUs belonging to Xanthomonadaceae and Rhizobium, together representing 50% of the relative bacterial abundance, as consistently associated with the wood substrate, regardless of fungal presence. Moreover, after 12 weeks, the bacterial community composition based on relative abundance was significantly modified by the presence of the white-rot fungus. Effectively, members of the Burkholderia genus were always associated with P.chrysosporium, representing potential taxonomic bioindicators of the white-rot mycosphere.
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Affiliation(s)
- Vincent Hervé
- Interactions Arbres - Microorganismes, UMR1136, INRA, Champenoux, France; Interactions Arbres - Microorganismes, UMR1136, Université de Lorraine, Vandoeuvre-lès-Nancy, France
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363
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Shi Y, Chai L, Tang C, Yang Z, Zheng Y, Chen Y, Jing Q. Biochemical investigation of kraft lignin degradation by Pandoraea sp. B-6 isolated from bamboo slips. Bioprocess Biosyst Eng 2013; 36:1957-65. [PMID: 23877715 PMCID: PMC3825317 DOI: 10.1007/s00449-013-0972-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/09/2013] [Indexed: 11/30/2022]
Abstract
Kraft lignin (KL) is the major pollutant in black liquor. The bacterial strain Pandoraea sp. B-6 was able to degrade KL without any co-substrate under high alkaline conditions. At least 38.2 % of chemical oxygen demand and 41.6 % of color were removed in 7 days at concentrations from 1 to 6 g L(-1). The optimum pH for KL degradation was 10 and the optimum temperature was 30 °C. The greatest activities of 2,249.2 U L(-1) for manganese peroxidase and 1,120.6 U L(-1) for laccase were detected on the third and fifth day at pH 10, respectively. Many small molecules, such as cinnamic acid, ferulic acid, 2-hydroxy benzyl alcohol, and vanillyl methyl ketone, were formed during the period of KL degradation based on GC-MS analysis. These results indicate that this strain has great potential for biotreatment of black liquor.
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Affiliation(s)
- Yan Shi
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
| | - Liyuan Chai
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
- Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution, Changsha, 410017 People’s Republic of China
| | - Chongjian Tang
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
- Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution, Changsha, 410017 People’s Republic of China
| | - Zhihui Yang
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
- Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution, Changsha, 410017 People’s Republic of China
| | - Yu Zheng
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
| | - Yuehui Chen
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
| | - Qingxiu Jing
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
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364
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Vandroemme J, Cottyn B, Baeyen S, De Vos P, Maes M. Draft genome sequence of Xanthomonas fragariae reveals reductive evolution and distinct virulence-related gene content. BMC Genomics 2013; 14:829. [PMID: 24274055 PMCID: PMC4046712 DOI: 10.1186/1471-2164-14-829] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 11/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU. It is taxonomically and metabolically distinct within the genus Xanthomonas, and known for its host specificity. As part of a broader pathogenicity study, the genome of a Belgian, virulent Xf strain (LMG 25863) was assembled to draft status and examined for its pathogenicity related gene content. RESULTS The Xf draft genome (4.2 Mb) was considerably smaller than most known Xanthomonas genomes (~5 Mb). Only half of the genes coding for TonB-dependent transporters and cell-wall degrading enzymes that are typically present in other Xanthomonas genomes, were found in Xf. Other missing genes/regions with a possible impact on its plant-host interaction were: i) the three loci for xylan degradation and metabolism, ii) a locus coding for a ß-ketoadipate phenolics catabolism pathway, iii) xcs, one of two Type II Secretion System coding regions in Xanthomonas, and iv) the genes coding for the glyoxylate shunt pathway. Conversely, the Xf genome revealed a high content of externally derived DNA and several uncommon, possibly virulence-related features: a Type VI Secretion System, a second Type IV Secretion System and a distinct Type III Secretion System effector repertoire comprised of multiple rare effectors and several putative new ones. CONCLUSIONS The draft genome sequence of LMG 25863 confirms the distinct phylogenetic position of Xf within the genus Xanthomonas and reveals a patchwork of both lost and newly acquired genomic features. These features may help explain the specific, mostly endophytic association of Xf with the strawberry plant.
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Affiliation(s)
- Joachim Vandroemme
- />Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit - Crop Protection, Merelbeke, Belgium
- />Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent, 9000 Belgium
| | - Bart Cottyn
- />Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit - Crop Protection, Merelbeke, Belgium
| | - Steve Baeyen
- />Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit - Crop Protection, Merelbeke, Belgium
| | - Paul De Vos
- />Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent, 9000 Belgium
| | - Martine Maes
- />Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit - Crop Protection, Merelbeke, Belgium
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365
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Chang YC, Choi D, Takamizawa K, Kikuchi S. Isolation of Bacillus sp. strains capable of decomposing alkali lignin and their application in combination with lactic acid bacteria for enhancing cellulase performance. BIORESOURCE TECHNOLOGY 2013; 152:429-36. [PMID: 24316485 DOI: 10.1016/j.biortech.2013.11.032] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/11/2013] [Accepted: 11/13/2013] [Indexed: 05/24/2023]
Abstract
Effective biological pretreatment method for enhancing cellulase performance was investigated. Two alkali lignin-degrading bacteria were isolated from forest soils in Japan and named CS-1 and CS-2. 16S rDNA sequence analysis indicated that CS-1 and CS-2 were Bacillus sp. Strains CS-1 and CS-2 displayed alkali lignin degradation capability. With initial concentrations of 0.05-2.0 g L(-1), at least 61% alkali lignin could be degraded within 48 h. High laccase activities were observed in crude enzyme extracts from the isolated strains. This result indicated that alkali lignin degradation was correlated with laccase activities. Judging from the net yields of sugars after enzymatic hydrolysis, the most effective pretreatment method for enhancing cellulase performance was a two-step processing procedure (pretreatment using Bacillus sp. CS-1 followed by lactic acid bacteria) at 68.6%. These results suggest that the two-step pretreatment procedure is effective at accelerating cellulase performance.
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Affiliation(s)
- Young-Cheol Chang
- Division of Applied Sciences, College of Environmental Technology, Graduate School of Engineering, Muroran Institute of Technology, 27-1 Mizumoto, Muroran 050-8585, Hokkaido, Japan.
| | - Dubok Choi
- Department of Pharmacy, College of Pharmacy, Chungbuk National University, Cheongju 361-763, Republic of Korea.
| | - Kazuhiro Takamizawa
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Shintaro Kikuchi
- Division of Applied Sciences, College of Environmental Technology, Graduate School of Engineering, Muroran Institute of Technology, 27-1 Mizumoto, Muroran 050-8585, Hokkaido, Japan
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366
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Ni J, Tokuda G. Lignocellulose-degrading enzymes from termites and their symbiotic microbiota. Biotechnol Adv 2013; 31:838-50. [DOI: 10.1016/j.biotechadv.2013.04.005] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 04/10/2013] [Accepted: 04/15/2013] [Indexed: 01/17/2023]
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367
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Margot J, Bennati-Granier C, Maillard J, Blánquez P, Barry DA, Holliger C. Bacterial versus fungal laccase: potential for micropollutant degradation. AMB Express 2013; 3:63. [PMID: 24152339 PMCID: PMC3819643 DOI: 10.1186/2191-0855-3-63] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 11/10/2022] Open
Abstract
Relatively high concentrations of micropollutants in municipal wastewater treatment plant (WWTP) effluents underscore the necessity to develop additional treatment steps prior to discharge of treated wastewater. Microorganisms that produce unspecific oxidative enzymes such as laccases are a potential means to improve biodegradation of these compounds. Four strains of the bacterial genus Streptomyces (S. cyaneus, S. ipomoea, S. griseus and S. psammoticus) and the white-rot fungus Trametes versicolor were studied for their ability to produce active extracellular laccase in biologically treated wastewater with different carbon sources. Among the Streptomyces strains evaluated, only S. cyaneus produced extracellular laccase with sufficient activity to envisage its potential use in WWTPs. Laccase activity produced by T. versicolor was more than 20 times greater, the highest activity being observed with ash branches as the sole carbon source. The laccase preparation of S. cyaneus (abbreviated LSc) and commercial laccase from T. versicolor (LTv) were further compared in terms of their activity at different pH and temperatures, their stability, their substrate range, and their micropollutant oxidation efficiency. LSc and LTv showed highest activities under acidic conditions (around pH 3 to 5), but LTv was active over wider pH and temperature ranges than LSc, especially at near-neutral pH and between 10 and 25°C (typical conditions found in WWTPs). LTv was also less affected by pH inactivation. Both laccase preparations oxidized the three micropollutants tested, bisphenol A, diclofenac and mefenamic acid, with faster degradation kinetics observed for LTv. Overall, T. versicolor appeared to be the better candidate to remove micropollutants from wastewater in a dedicated post-treatment step.
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368
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Deangelis KM, Sharma D, Varney R, Simmons B, Isern NG, Markilllie LM, Nicora C, Norbeck AD, Taylor RC, Aldrich JT, Robinson EW. Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1. Front Microbiol 2013; 4:280. [PMID: 24065962 PMCID: PMC3777014 DOI: 10.3389/fmicb.2013.00280] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/29/2013] [Indexed: 01/05/2023] Open
Abstract
Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, where bacteria using oxygen-independent enzymes likely play an important role in decomposition. We have used transcriptomics and proteomics to examine the observed increased growth of SCF1 grown on media amended with lignin compared to unamended growth. Proteomics suggested accelerated xylose uptake and metabolism under lignin-amended growth, with up-regulation of proteins involved in lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase (GST) proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. This suggested the use of lignin as terminal electron acceptor. We detected significant lignin degradation over time by absorbance, and also used metabolomics to demonstrate moderately significant decreased xylose concentrations as well as increased metabolic products acetate and formate in stationary phase in lignin-amended compared to unamended growth conditions. Our data show the advantages of a multi-omics approach toward providing insights as to how lignin may be used in nature by microorganisms coping with poor carbon availability.
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Affiliation(s)
- Kristen M Deangelis
- Department of Microbiology, University of Massachusetts Amherst Amherst, MA, USA
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369
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Barry KP, Taylor EA. Characterizing the promiscuity of LigAB, a lignin catabolite degrading extradiol dioxygenase from Sphingomonas paucimobilis SYK-6. Biochemistry 2013; 52:6724-36. [PMID: 23977959 DOI: 10.1021/bi400665t] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
LigAB from Sphingomonas paucimobilis SYK-6 is the only structurally characterized dioxygenase of the largely uncharacterized superfamily of Type II extradiol dioxygenases (EDO). This enzyme catalyzes the oxidative ring-opening of protocatechuate (3,4-dihydroxybenzoic acid or PCA) in a pathway allowing the degradation of lignin derived aromatic compounds (LDACs). LigAB has also been shown to utilize two other LDACs from the same metabolic pathway as substrates, gallate, and 3-O-methyl gallate; however, kcat/KM had not been reported for any of these compounds. In order to assess the catalytic efficiency and get insights into the observed promiscuity of this enzyme, steady-state kinetic analyses were performed for LigAB with these and a library of related compounds. The dioxygenation of PCA by LigAB was highly efficient, with a kcat of 51 s(-1) and a kcat/KM of 4.26 × 10(6) M(-1)s(-1). LigAB demonstrated the ability to use a variety of catecholic molecules as substrates beyond the previously identified gallate and 3-O-methyl gallate, including 3,4-dihydroxybenzamide, homoprotocatechuate, catechol, and 3,4-dihydroxybenzonitrile. Interestingly, 3,4-dihydroxybenzamide (DHBAm) behaves in a manner similar to that of the preferred benzoic acid substrates, with a kcat/Km value only ∼4-fold lower than that for gallate and ∼10-fold higher than that for 3-O-methyl gallate. All of these most active substrates demonstrate mechanistic inactivation of LigAB. Additionally, DHBAm exhibits potent product inhibition that leads to an inactive enzyme, being more highly deactivating at lower substrate concentration, a phenomena that, to our knowledge, has not been reported for another dioxygenase substrate/product pair. These results provide valuable catalytic insight into the reactions catalyzed by LigAB and make it the first Type II EDO that is fully characterized both structurally and kinetically.
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Affiliation(s)
- Kevin P Barry
- Department of Chemistry, Wesleyan University , 52 Lawn Avenue, Middletown, Connecticut 06459, United States
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370
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Scully ED, Geib SM, Hoover K, Tien M, Tringe SG, Barry KW, Glavina del Rio T, Chovatia M, Herr JR, Carlson JE. Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle. PLoS One 2013; 8:e73827. [PMID: 24023907 PMCID: PMC3762729 DOI: 10.1371/journal.pone.0073827] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 07/25/2013] [Indexed: 11/23/2022] Open
Abstract
The Asian longhorned beetle (Anoplophoraglabripennis) is an invasive, wood-boring pest that thrives in the heartwood of deciduous tree species. A large impediment faced by A. glabripennis as it feeds on woody tissue is lignin, a highly recalcitrant biopolymer that reduces access to sugars and other nutrients locked in cellulose and hemicellulose. We previously demonstrated that lignin, cellulose, and hemicellulose are actively deconstructed in the beetle gut and that the gut harbors an assemblage of microbes hypothesized to make significant contributions to these processes. While lignin degrading mechanisms have been well characterized in pure cultures of white rot basidiomycetes, little is known about such processes in microbial communities associated with wood-feeding insects. The goals of this study were to develop a taxonomic and functional profile of a gut community derived from an invasive population of larval A. glabripennis collected from infested host trees and to identify genes that could be relevant for the digestion of woody tissue and nutrient acquisition. To accomplish this goal, we taxonomically and functionally characterized the A. glabripennis midgut microbiota through amplicon and shotgun metagenome sequencing and conducted a large-scale comparison with the metagenomes from a variety of other herbivore-associated communities. This analysis distinguished the A. glabripennis larval gut metagenome from the gut communities of other herbivores, including previously sequenced termite hindgut metagenomes. Genes encoding enzymes were identified in the A. glabripennis gut metagenome that could have key roles in woody tissue digestion including candidate lignin degrading genes (laccases, dye-decolorizing peroxidases, novel peroxidases and β-etherases), 36 families of glycoside hydrolases (such as cellulases and xylanases), and genes that could facilitate nutrient recovery, essential nutrient synthesis, and detoxification. This community could serve as a reservoir of novel enzymes to enhance industrial cellulosic biofuels production or targets for novel control methods for this invasive and highly destructive insect.
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Affiliation(s)
- Erin D. Scully
- Intercollege Graduate Program in Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research Unit, United States Department of Agriculture Agriculture Research Service Pacific Basin Agricultural Research Center, Hilo, Hawaii, United States of America
| | - Kelli Hoover
- Department of Entomology and Center for Chemical Ecology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Ming Tien
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Susannah G. Tringe
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Kerrie W. Barry
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Tijana Glavina del Rio
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Mansi Chovatia
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Joshua R. Herr
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - John E. Carlson
- The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, South Korea
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371
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Characterization of the bacterial community associated with larvae and adults of Anoplophora chinensis collected in Italy by culture and culture-independent methods. BIOMED RESEARCH INTERNATIONAL 2013; 2013:420287. [PMID: 24069601 PMCID: PMC3771249 DOI: 10.1155/2013/420287] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/09/2013] [Indexed: 11/25/2022]
Abstract
The wood-boring beetle Anoplophora chinensis Forster, native to China, has recently spread to North America and Europe causing serious damage to ornamental and forest trees. The gut microbial community associated with these xylophagous beetles is of interest for potential biotechnological applications in lignocellulose degradation and development of pest-control measures. In this study the gut bacterial community of larvae and adults of A. chinensis, collected from different host trees in North Italy, was investigated by both culture and culture-independent methods. Larvae and adults harboured a moderately diverse bacterial community, dominated by Proteobacteria, Actinobacteria, and Firmicutes. The gammaproteobacterial family Enterobacteriaceae (genera Gibbsiella, Enterobacter, Raoultella, and Klebsiella) was the best represented. The abundance of such bacteria in the insect gut is likely due to the various metabolic abilities of Enterobacteriaceae, including fermentation of carbohydrates derived from lignocellulose degradation and contribution to nitrogen intake by nitrogen-fixing activity. In addition, bacteria previously shown to have some lignocellulose-degrading activity were detected at a relatively low level in the gut. These bacteria possibly act synergistically with endogenous and fungal enzymes in lignocellulose breakdown. The detection of actinobacterial symbionts could be explained by a possible role in the detoxification of secondary plant metabolites and/or protection against pathogens.
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372
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Uroz S, Courty PE, Pierrat JC, Peter M, Buée M, Turpault MP, Garbaye J, Frey-Klett P. Functional profiling and distribution of the forest soil bacterial communities along the soil mycorrhizosphere continuum. MICROBIAL ECOLOGY 2013; 66:404-15. [PMID: 23455431 DOI: 10.1007/s00248-013-0199-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 02/08/2013] [Indexed: 05/09/2023]
Abstract
An ectomycorrhiza is a multitrophic association between a tree root, an ectomycorrhizal fungus, free-living fungi and the associated bacterial communities. Enzymatic activities of ectomycorrhizal root tips are therefore result of the contribution from different partners of the symbiotic organ. However, the functional potential of the fungus-associated bacterial communities remains unknown. In this study, a collection of 80 bacterial strains randomly selected and isolated from a soil-ectomycorrhiza continuum (oak-Scleroderma citrinum ectomycorrhizas, the ectomycorrhizosphere and the surrounding bulk soil) were characterized. All the bacterial isolates were identified by partial 16S rRNA gene sequences as members of the genera Burkholderia, Collimonas, Dyella, Mesorhizobium, Pseudomonas, Rhizobium and Sphingomonas. The bacterial strains were then assayed for β-xylosidase, β-glucosidase, N-acetyl-hexosaminidase, β-glucuronidase, cellobiohydrolase, phosphomonoesterase, leucine-aminopeptidase and laccase activities, chitin solubilization and auxin production. Using these bioassays, we demonstrated significant differences in the functional distribution of the bacterial communities living in the different compartments of the soil-ectomycorrhiza continuum. The surrounding bulk soil was significantly enriched in bacterial isolates capable of hydrolysing cellobiose and N-acetylglucosamine. In contrast, the ectomycorrhizosphere appeared significantly enriched in bacterial isolates capable of hydrolysing glucopyranoside and chitin. Notably, chitinase and laccase activities were found only in bacterial isolates belonging to the Collimonas and Pseudomonas genera. Overall, the results suggest that the ectomycorrhizal fungi favour specific bacterial communities with contrasting functional characteristics from the surrounding soil.
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Affiliation(s)
- S Uroz
- INRA, UMR1136 INRA-Nancy Université Interactions Arbres-Microorganismes, Centre INRA de Nancy, 54280, Champenoux, France.
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373
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Tan K, Chang C, Cuff M, Osipiuk J, Landorf E, Mack JC, Zerbs S, Joachimiak A, Collart FR. Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids. Proteins 2013; 81:1709-26. [PMID: 23606130 DOI: 10.1002/prot.24305] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 03/12/2013] [Accepted: 03/28/2013] [Indexed: 11/10/2022]
Abstract
Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins.
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Affiliation(s)
- Kemin Tan
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, 60439; The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, Illinois, 60439; Structural Biology Center, Argonne National Laboratory, Lemont, Illinois, 60439
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374
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D'haeseleer P, Gladden JM, Allgaier M, Chain PSG, Tringe SG, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, Paša-Tolić L, Hugenholtz P, Simmons BA, Singer SW. Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS One 2013; 8:e68465. [PMID: 23894306 PMCID: PMC3716776 DOI: 10.1371/journal.pone.0068465] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 05/29/2013] [Indexed: 12/02/2022] Open
Abstract
Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the little-studied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify >3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.
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Affiliation(s)
- Patrik D'haeseleer
- Joint BioEnergy Institute, Emeryville, California, United States of America.
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375
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Niemi P, Aura AM, Maukonen J, Smeds AI, Mattila I, Niemelä K, Tamminen T, Faulds CB, Buchert J, Poutanen K. Interactions of a lignin-rich fraction from brewer's spent grain with gut microbiota in vitro. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:6754-6762. [PMID: 23768078 DOI: 10.1021/jf401738x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Lignin is a constituent of plant cell walls and thus is classified as part of dietary fiber. However, little is known about the role of lignin in gastrointestinal fermentation. In this work, a lignin-rich fraction was prepared from brewer's spent grain and subjected to an in vitro colon model to study its potential bioconversions and interactions with fecal microbiota. No suppression of microbial conversion by the fraction was observed in the colon model, as measured as short-chain fatty acid production. Furthermore, no inhibition on the growth was observed when the fraction was incubated with strains of lactobacilli and bifidobacteria. In fact, the lignin-rich fraction enabled bifidobacteria to survive longer than with glucose. Several transiently appearing phenolic compounds, very likely originating from lignin, were observed during the fermentation. This would indicate that the gut microbiota was able to partially degrade lignin and metabolize the released compounds.
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Affiliation(s)
- Piritta Niemi
- Bio and Process Technology, VTT Technical Research Centre of Finland , P.O. Box 1000, FI-02044 VTT Espoo, Finland
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376
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Genome Sequence of Streptomyces viridosporus Strain T7A ATCC 39115, a Lignin-Degrading Actinomycete. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00416-13. [PMID: 23833133 PMCID: PMC3703594 DOI: 10.1128/genomea.00416-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We announce the availability of the genome sequence of Streptomyces viridosporus strain T7A ATCC 39115, a plant biomass-degrading actinomycete. This bacterium is of special interest because of its capacity to degrade lignin, an underutilized component of plants in the context of bioenergy. It has a full complement of genes for plant biomass catabolism.
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377
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Sherif M, Waung D, Korbeci B, Mavisakalyan V, Flick R, Brown G, Abou-Zaid M, Yakunin AF, Master ER. Biochemical studies of the multicopper oxidase (small laccase) from Streptomyces coelicolor using bioactive phytochemicals and site-directed mutagenesis. Microb Biotechnol 2013; 6:588-97. [PMID: 23815400 PMCID: PMC3918160 DOI: 10.1111/1751-7915.12068] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 11/30/2022] Open
Abstract
Multicopper oxidases can act on a broad spectrum of phenolic and non-phenolic compounds. These enzymes include laccases, which are widely distributed in plants and fungi, and were more recently identified in bacteria. Here, we present the results of biochemical and mutational studies of small laccase (SLAC), a multicopper oxidase from Streptomyces coelicolor (SCO6712). In addition to typical laccase substrates, SLAC was tested using phenolic compounds that exhibit antioxidant activity. SLAC showed oxidase activity against 12 of 23 substrates tested, including caffeic acid, ferulic acid, resveratrol, quercetin, morin, kaempferol and myricetin. The kinetic parameters of SLAC were determined for 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid), 2,6-dimethoxyphenol, quercetin, morin and myricetin, and maximum reaction rates were observed with myricetin, where kcat and Km values at 60°C were 8.1 (± 0.8) s−1 and 0.9 (± 0.3) mM respectively. SLAC had a broad pH optimum for activity (between pH 4 and 8) and temperature optimum at 60–70°C. It demonstrated remarkable thermostability with a half-life of over 10 h at 80°C and over 7 h at 90°C. Site-directed mutagenesis revealed 17 amino acid residues important for SLAC activity including the 10 His residues involved in copper coordination. Most notably, the Y229A and Y230A mutant proteins showed over 10-fold increase in activity compared with the wild-type SLAC, which was correlated to higher copper incorporation, while kinetic analyses with S929A predicts localization of this residue near the meta-position of aromatic substrates. Funding Information Funding for this research was provided by the Government of Ontario for the project ‘FFABnet: Functionalized Fibre and Biochemicals’ (ORF-RE-05-005), and the Natural Sciences and Engineering Research Council of Canada.
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Affiliation(s)
- Mohammed Sherif
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
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378
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van der Wal A, Geydan TD, Kuyper TW, de Boer W. A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes. FEMS Microbiol Rev 2013; 37:477-94. [DOI: 10.1111/1574-6976.12001] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 08/02/2012] [Accepted: 08/21/2012] [Indexed: 12/24/2022] Open
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379
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Microbial brokers of insect-plant interactions revisited. J Chem Ecol 2013; 39:952-61. [PMID: 23793897 DOI: 10.1007/s10886-013-0308-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/01/2013] [Accepted: 06/06/2013] [Indexed: 12/22/2022]
Abstract
Recent advances in sequencing methods have transformed the field of microbial ecology, making it possible to determine the composition and functional capabilities of uncultured microorganisms. These technologies have been instrumental in the recognition that resident microorganisms can have profound effects on the phenotype and fitness of their animal hosts by modulating the animal signaling networks that regulate growth, development, behavior, etc. Against this backdrop, this review assesses the impact of microorganisms on insect-plant interactions, in the context of the hypothesis that microorganisms are biochemical brokers of plant utilization by insects. There is now overwhelming evidence for a microbial role in insect utilization of certain plant diets with an extremely low or unbalanced nutrient content. Specifically, microorganisms enable insect utilization of plant sap by synthesizing essential amino acids. They also can broker insect utilization of plant products of extremely high lignocellulose content, by enzymatic breakdown of complex plant polysaccharides, nitrogen fixation, and sterol synthesis. However, the experimental evidence for microbial-mediated detoxification of plant allelochemicals is limited. The significance of microorganisms as brokers of plant utilization by insects is predicted to vary, possibly widely, as a result of potentially complex interactions between the composition of the microbiota and the diet and insect developmental age or genotype. For every insect species feeding on plant material, the role of resident microbiota as biochemical brokers of plant utilization is a testable hypothesis.
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380
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Metagenomic analysis of a tropical composting operation at the são paulo zoo park reveals diversity of biomass degradation functions and organisms. PLoS One 2013; 8:e61928. [PMID: 23637931 PMCID: PMC3637033 DOI: 10.1371/journal.pone.0061928] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/15/2013] [Indexed: 12/19/2022] Open
Abstract
Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the São Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders.
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381
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Huang XF, Bakker MG, Judd TM, Reardon KF, Vivanco JM. Variations in diversity and richness of gut bacterial communities of termites (Reticulitermes flavipes) fed with grassy and woody plant substrates. MICROBIAL ECOLOGY 2013; 65:531-6. [PMID: 23529653 DOI: 10.1007/s00248-013-0219-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/12/2013] [Indexed: 05/23/2023]
Abstract
Diets shape the animal gut microbiota, although the relationships between diets and the structure of the gut microbial community are not yet well understood. The gut bacterial communities of Reticulitermes flavipes termites fed on four individual plant biomasses with different degrees of recalcitrance to biodegradation were investigated by 16S rRNA pyrosequencing analysis. The termite gut bacterial communities could be differentiated between grassy and woody diets, and among grassy diets (corn stover vs. sorghum). The majority of bacterial taxa were shared across all diets, but each diet significantly enriched some taxa. Interestingly, the diet of corn stover reduced gut bacterial richness and diversity compared to other diets, and this may be related to the lower recalcitrance of this biomass to degradation.
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Affiliation(s)
- Xing-Feng Huang
- Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO 80523-1173, USA
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382
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Levasseur A, Drula E, Lombard V, Coutinho PM, Henrissat B. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:41. [PMID: 23514094 PMCID: PMC3620520 DOI: 10.1186/1754-6834-6-41] [Citation(s) in RCA: 768] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 03/11/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Since its inception, the carbohydrate-active enzymes database (CAZy; http://www.cazy.org) has described the families of enzymes that cleave or build complex carbohydrates, namely the glycoside hydrolases (GH), the polysaccharide lyases (PL), the carbohydrate esterases (CE), the glycosyltransferases (GT) and their appended non-catalytic carbohydrate-binding modules (CBM). The recent discovery that members of families CBM33 and family GH61 are in fact lytic polysaccharide monooxygenases (LPMO), demands a reclassification of these families into a suitable category. RESULTS Because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with (LPMO), we have decided to join the families of lignin degradation enzymes to the LPMO families and launch a new CAZy class that we name "Auxiliary Activities" in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion. Comparative analyses of these auxiliary activities in 41 fungal genomes reveal a pertinent division of several fungal groups and subgroups combining their phylogenetic origin and their nutritional mode (white vs. brown rot). CONCLUSIONS The new class introduced in the CAZy database extends the traditional CAZy families, and provides a better coverage of the full extent of the lignocellulose breakdown machinery.
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Affiliation(s)
- Anthony Levasseur
- INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, ESIL Polytech Marseille, 163 avenue de Luminy, CP 925, 13288, Marseille, Cedex 09, France
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Aix-Marseille Université, 163 Avenue de Luminy, Marseille, 13288, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Aix-Marseille Université, 163 Avenue de Luminy, Marseille, 13288, France
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Aix-Marseille Université, 163 Avenue de Luminy, Marseille, 13288, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Aix-Marseille Université, 163 Avenue de Luminy, Marseille, 13288, France
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383
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Huang XF, Santhanam N, Badri DV, Hunter WJ, Manter DK, Decker SR, Vivanco JM, Reardon KF. Isolation and characterization of lignin-degrading bacteria from rainforest soils. Biotechnol Bioeng 2013; 110:1616-26. [PMID: 23297115 DOI: 10.1002/bit.24833] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 11/21/2012] [Accepted: 12/17/2012] [Indexed: 11/09/2022]
Abstract
The deconstruction of lignin to enhance the release of fermentable sugars from plant cell walls presents a challenge for biofuels production from lignocellulosic biomass. The discovery of novel lignin-degrading enzymes from bacteria could provide advantages over fungal enzymes in terms of their production and relative ease of protein engineering. In this study, 140 bacterial strains isolated from soils of a biodiversity-rich rainforest in Peru were screened based on their oxidative activity on ABTS, a laccase substrate. Strain C6 (Bacillus pumilus) and strain B7 (Bacillus atrophaeus) were selected for their high laccase activity and identified by 16S rDNA analysis. Strains B7 and C6 degraded fragments of Kraft lignin and the lignin model dimer guaiacylglycerol-β-guaiacyl ether, the most abundant linkage in lignin. Finally, LC-MS analysis of incubations of strains B7 and C6 with poplar biomass in rich and minimal media revealed that a higher number of compounds were released in the minimal medium than in the rich one. These findings provide important evidence that bacterial enzymes can degrade and/or modify lignin and contribute to the release of fermentable sugars from lignocellulose.
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Affiliation(s)
- Xing-Feng Huang
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado 80523-1370, USA
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384
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Microbial mechanisms mediating increased soil C storage under elevated atmospheric N deposition. Appl Environ Microbiol 2012; 79:1191-9. [PMID: 23220961 DOI: 10.1128/aem.03156-12] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Future rates of anthropogenic N deposition can slow the cycling and enhance the storage of C in forest ecosystems. In a northern hardwood forest ecosystem, experimental N deposition has decreased the extent of forest floor decay, leading to increased soil C storage. To better understand the microbial mechanisms mediating this response, we examined the functional genes derived from communities of actinobacteria and fungi present in the forest floor using GeoChip 4.0, a high-throughput functional-gene microarray. The compositions of functional genes derived from actinobacterial and fungal communities was significantly altered by experimental nitrogen deposition, with more heterogeneity detected in both groups. Experimental N deposition significantly decreased the richness and diversity of genes involved in the depolymerization of starch (∼12%), hemicellulose (∼16%), cellulose (∼16%), chitin (∼15%), and lignin (∼16%). The decrease in richness occurred across all taxonomic groupings detected by the microarray. The compositions of genes encoding oxidoreductases, which plausibly mediate lignin decay, were responsible for much of the observed dissimilarity between actinobacterial communities under ambient and experimental N deposition. This shift in composition and decrease in richness and diversity of genes encoding enzymes that mediate the decay process has occurred in parallel with a reduction in the extent of decay and accumulation of soil organic matter. Our observations indicate that compositional changes in actinobacterial and fungal communities elicited by experimental N deposition have functional implications for the cycling and storage of carbon in forest ecosystems.
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385
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Sinsabaugh RL, Follstad Shah JJ. Ecoenzymatic Stoichiometry and Ecological Theory. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2012. [DOI: 10.1146/annurev-ecolsys-071112-124414] [Citation(s) in RCA: 397] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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386
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Fang W, Fang Z, Zhou P, Chang F, Hong Y, Zhang X, Peng H, Xiao Y. Evidence for lignin oxidation by the giant panda fecal microbiome. PLoS One 2012; 7:e50312. [PMID: 23209704 PMCID: PMC3508987 DOI: 10.1371/journal.pone.0050312] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/18/2012] [Indexed: 11/19/2022] Open
Abstract
The digestion of lignin and lignin-related phenolic compounds from bamboo by giant pandas has puzzled scientists because of the lack of lignin-degrading genes in the genome of the bamboo-feeding animals. We constructed a 16S rRNA gene library from the microorganisms derived from the giant panda feces to identify the possibility for the presence of potential lignin-degrading bacteria. Phylogenetic analysis showed that the phylotypes of the intestinal bacteria were affiliated with the phyla Proteobacteria (53%) and Firmicutes (47%). Two phylotypes were affiliated with the known lignin-degrading bacterium Pseudomonas putida and the mangrove forest bacteria. To test the hypothesis that microbes in the giant panda gut help degrade lignin, a metagenomic library of the intestinal bacteria was constructed and screened for clones that contained genes encoding laccase, a lignin-degrading related enzyme. A multicopper oxidase gene, designated as lac51, was identified from a metagenomic clone. Sequence analysis and copper content determination indicated that Lac51 is a laccase rather than a metallo-oxidase and may work outside its original host cell because it has a TAT-type signal peptide and a transmembrane segment at its N-terminus. Lac51 oxidizes a variety of lignin-related phenolic compounds, including syringaldazine, 2,6-dimethoxyphenol, ferulic acid, veratryl alcohol, guaiacol, and sinapinic acid at conditions that simulate the physiologic environment in giant panda intestines. Furthermore, in the presence of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), syringic acid, or ferulic acid as mediators, the oxidative ability of Lac51 on lignin was promoted. The absorbance of lignin at 445 nm decreased to 36% for ABTS, 51% for syringic acid, and 51% for ferulic acid after incubation for 10 h. Our findings demonstrate that the intestinal bacteria of giant pandas may facilitate the oxidation of lignin moieties, thereby clarifying the digestion of bamboo lignin by the animal.
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Affiliation(s)
- Wei Fang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Peng Zhou
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Fei Chang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Yuzhi Hong
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Xuecheng Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Hui Peng
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
- * E-mail:
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387
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Michalska K, Chang C, Mack JC, Zerbs S, Joachimiak A, Collart FR. Characterization of transport proteins for aromatic compounds derived from lignin: benzoate derivative binding proteins. J Mol Biol 2012; 423:555-75. [PMID: 22925578 PMCID: PMC3836681 DOI: 10.1016/j.jmb.2012.08.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 07/27/2012] [Accepted: 08/20/2012] [Indexed: 10/28/2022]
Abstract
In vitro growth experiments have demonstrated that aromatic compounds derived from lignin can be metabolized and represent a major carbon resource for many soil bacteria. However, the proteins that mediate the movement of these metabolites across the cell membrane have not been thoroughly characterized. To address this deficiency, we used a library representative of lignin degradation products and a thermal stability screen to determine ligand specificity for a set of solute-binding proteins (SBPs) from ATP-binding cassette (ABC) transporters. The ligand mapping process identified a set of proteins from Alphaproteobacteria that recognize various benzoate derivatives. Seven high-resolution crystal structures of these proteins in complex with four different aromatic compounds were obtained. The protein-ligand complexes provide details of molecular recognition that can be used to infer binding specificity. This structure-function characterization provides new insight for the biological roles of these ABC transporters and their SBPs, which had been previously annotated as branched-chain amino-acid-binding proteins. The knowledge derived from the crystal structures provides a foundation for development of sequence-based methods to predict the ligand specificity of other uncharacterized transporters. These results also demonstrate that Alphaproteobacteria possess a diverse set of transport capabilities for lignin-derived compounds. Characterization of this new class of transporters improves genomic annotation projects and provides insight into the metabolic potential of soil bacteria.
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Affiliation(s)
- Karolina Michalska
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Changsoo Chang
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL 60439, USA
- Structural Biology Center, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Jamey C. Mack
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Sarah Zerbs
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Andrzej Joachimiak
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL 60439, USA
- Structural Biology Center, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Frank R. Collart
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
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388
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Gasser CA, Hommes G, Schäffer A, Corvini PFX. Multi-catalysis reactions: new prospects and challenges of biotechnology to valorize lignin. Appl Microbiol Biotechnol 2012; 95:1115-34. [PMID: 22782247 DOI: 10.1007/s00253-012-4178-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 05/15/2012] [Accepted: 05/15/2012] [Indexed: 11/28/2022]
Abstract
Considerable effort has been dedicated to the chemical depolymerization of lignin, a biopolymer constituting a possible renewable source for aromatic value-added chemicals. However, these efforts yielded limited success up until now. Efficient lignin conversion might necessitate novel catalysts enabling new types of reactions. The use of multiple catalysts, including a combination of biocatalysts, might be necessary. New perspectives for the combination of bio- and inorganic catalysts in one-pot reactions are emerging, thanks to green chemistry-driven advances in enzyme engineering and immobilization and new chemical catalyst design. Such combinations could offer several advantages, especially by reducing time and yield losses associated with the isolation and purification of the reaction products, but also represent a big challenge since the optimal reaction conditions of bio- and chemical catalysis reactions are often different. This mini-review gives an overview of bio- and inorganic catalysts having the potential to be used in combination for lignin depolymerization. We also discuss key aspects to consider when combining these catalysts in one-pot reactions.
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Affiliation(s)
- Christoph A Gasser
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz, 4132, Switzerland
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389
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Taylor C, Hardiman E, Ahmad M, Sainsbury P, Norris P, Bugg T. Isolation of bacterial strains able to metabolize lignin from screening of environmental samples. J Appl Microbiol 2012; 113:521-30. [DOI: 10.1111/j.1365-2672.2012.05352.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 05/18/2012] [Accepted: 05/21/2012] [Indexed: 11/27/2022]
Affiliation(s)
- C.R. Taylor
- Department of Chemistry; University of Warwick; Coventry; UK
| | - E.M. Hardiman
- Department of Chemistry; University of Warwick; Coventry; UK
| | - M. Ahmad
- Department of Chemistry; University of Warwick; Coventry; UK
| | - P.D. Sainsbury
- Department of Chemistry; University of Warwick; Coventry; UK
| | - P.R. Norris
- School of Life Sciences; University of Warwick; Coventry; UK
| | - T.D.H. Bugg
- Department of Chemistry; University of Warwick; Coventry; UK
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390
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Scully ED, Hoover K, Carlson J, Tien M, Geib SM. Proteomic analysis of Fusarium solani isolated from the Asian longhorned beetle, Anoplophora glabripennis. PLoS One 2012; 7:e32990. [PMID: 22496740 PMCID: PMC3322136 DOI: 10.1371/journal.pone.0032990] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 02/05/2012] [Indexed: 11/20/2022] Open
Abstract
Wood is a highly intractable food source, yet many insects successfully colonize and thrive in this challenging niche. Overcoming the lignin barrier of wood is a key challenge in nutrient acquisition, but full depolymerization of intact lignin polymers has only been conclusively demonstrated in fungi and is not known to occur by enzymes produced by insects or bacteria. Previous research validated that lignocellulose and hemicellulose degradation occur within the gut of the wood boring insect, Anoplophora glabripennis (Asian longhorned beetle), and that a fungal species, Fusarium solani (ATCC MYA 4552), is consistently associated with the larval stage. While the nature of this relationship is unresolved, we sought to assess this fungal isolate's ability to degrade lignocellulose and cell wall polysaccharides and to extract nutrients from woody tissue. This gut-derived fungal isolate was inoculated onto a wood-based substrate and shotgun proteomics using Multidimensional Protein Identification Technology (MudPIT) was employed to identify 400 expressed proteins. Through this approach, we detected proteins responsible for plant cell wall polysaccharide degradation, including proteins belonging to 28 glycosyl hydrolase families and several cutinases, esterases, lipases, pectate lyases, and polysaccharide deacetylases. Proteinases with broad substrate specificities and ureases were observed, indicating that this isolate has the capability to digest plant cell wall proteins and recycle nitrogenous waste under periods of nutrient limitation. Additionally, several laccases, peroxidases, and enzymes involved in extracellular hydrogen peroxide production previously implicated in lignin depolymerization were detected. In vitro biochemical assays were conducted to corroborate MudPIT results and confirmed that cellulases, glycosyl hydrolases, xylanases, laccases, and Mn- independent peroxidases were active in culture; however, lignin- and Mn- dependent peroxidase activities were not detected While little is known about the role of filamentous fungi and their associations with insects, these findings suggest that this isolate has the endogenous potential to degrade lignocellulose and extract nutrients from woody tissue.
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Affiliation(s)
- Erin D. Scully
- Intercollege Program in Genetics, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kelli Hoover
- Department of Entomology, Center for Chemical Ecology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - John Carlson
- School of Forest Resources, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Bioenergy Science and Technology (World Class University), Chonnam National University, Buk-Gu, Gwangju, Korea
| | - Ming Tien
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research Unit, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, Hawaii, United States of America
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391
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Complete genome sequence of Sphingobium sp. strain SYK-6, a degrader of lignin-derived biaryls and monoaryls. J Bacteriol 2012; 194:534-5. [PMID: 22207743 DOI: 10.1128/jb.06254-11] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sphingobium sp. strain SYK-6 is able to grow on an extensive variety of lignin-derived biaryls and monoaryls, and the catabolic genes for these compounds are useful for the production of industrially valuable metabolites from lignin. Here we report the complete nucleotide sequence of the SYK-6 genome which consists of the 4,199,332-bp-long chromosome and the 148,801-bp-long plasmid.
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392
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Developing symbiotic consortia for lignocellulosic biofuel production. Appl Microbiol Biotechnol 2012; 93:1423-35. [PMID: 22278256 DOI: 10.1007/s00253-011-3762-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 11/12/2011] [Accepted: 11/14/2011] [Indexed: 10/14/2022]
Abstract
The search for petroleum alternatives has motivated intense research into biological breakdown of lignocellulose to produce liquid fuels such as ethanol. Degradation of lignocellulose for biofuel production is a difficult process which is limited by, among other factors, the recalcitrance of lignocellulose and biological toxicity of the products. Consolidated bioprocessing has been suggested as an efficient and economical method of producing low value products from lignocellulose; however, it is not clear whether this would be accomplished more efficiently with a single organism or community of organisms. This review highlights examples of mixtures of microbes in the context of conceptual models for developing symbiotic consortia for biofuel production from lignocellulose. Engineering a symbiosis within consortia is a putative means of improving both process efficiency and stability relative to monoculture. Because microbes often interact and exist attached to surfaces, quorum sensing and biofilm formation are also discussed in terms of consortia development and stability. An engineered, symbiotic culture of multiple organisms may be a means of assembling a novel combination of metabolic capabilities that can efficiently produce biofuel from lignocellulose.
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393
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Ohta Y, Nishi S, Haga T, Tsubouchi T, Hasegawa R, Konishi M, Nagano Y, Tsuruwaka Y, Shimane Y, Mori K, Usui K, Suda E, Tsutsui K, Nishimoto A, Fujiwara Y, Maruyama T, Hatada Y. Screening and Phylogenetic Analysis of Deep-Sea Bacteria Capable of Metabolizing Lignin-Derived Aromatic Compounds. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ojms.2012.24021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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394
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Winter RT, van den Berg TE, Colpa DI, van Bloois E, Fraaije MW. Functionalization of oxidases with peroxidase activity creates oxiperoxidases: a new breed of hybrid enzyme capable of cascade chemistry. Chembiochem 2011; 13:252-8. [PMID: 22213198 DOI: 10.1002/cbic.201100639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Indexed: 11/09/2022]
Abstract
The covalent flavoprotein alditol oxidase (AldO) from Streptomyces coelicolor A3(2) was endowed with an extra catalytic functionality by fusing it to a microperoxidase. Purification of the construct resulted in the isolation of a synthetic bifunctional enzyme that was both fully covalently flavinylated and heminylated: an oxiperoxidase. Characterization revealed that both oxidase and peroxidase functionalities were active, with the construct functioning as a single-component xylitol biosensor. In an attempt to reduce the size of the oxidase-peroxidase fusion, we replaced portions of the native AldO sequence with the bacterial cytochrome c CXXCH heme-binding motif. By mutating only three residues of the AldO protein we were able to create a functional oxidase-peroxidase hybrid.
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Affiliation(s)
- Remko T Winter
- Laboratory of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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395
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Abstract
Genes encoding vanillin dehydrogenase (vdh) and vanillate O-demethylase (vanAB) were identified in Rhodococcus jostii RHA1 using gene disruption and enzyme activities. During growth on vanillin or vanillate, vanA was highly upregulated while vdh was not. This study contributes to our understanding of lignin degradation by RHA1 and other actinomycetes.
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396
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Bandounas L, Wierckx NJ, de Winde JH, Ruijssenaars HJ. Isolation and characterization of novel bacterial strains exhibiting ligninolytic potential. BMC Biotechnol 2011; 11:94. [PMID: 21995752 PMCID: PMC3212925 DOI: 10.1186/1472-6750-11-94] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 10/13/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To expand on the range of products which can be obtained from lignocellulosic biomass, the lignin component should be utilized as feedstock for value-added chemicals such as substituted aromatics, instead of being incinerated for heat and energy. Enzymes could provide an effective means for lignin depolymerization into products of interest. In this study, soil bacteria were isolated by enrichment on Kraft lignin and evaluated for their ligninolytic potential as a source of novel enzymes for waste lignin valorization. RESULTS Based on 16S rRNA gene sequencing and phenotypic characterization, the organisms were identified as Pandoraea norimbergensis LD001, Pseudomonas sp LD002 and Bacillus sp LD003. The ligninolytic capability of each of these isolates was assessed by growth on high-molecular weight and low-molecular weight lignin fractions, utilization of lignin-associated aromatic monomers and degradation of ligninolytic indicator dyes. Pandoraea norimbergensis LD001 and Pseudomonas sp. LD002 exhibited best growth on lignin fractions, but limited dye-decolourizing capacity. Bacillus sp. LD003, however, showed least efficient growth on lignin fractions but extensive dye-decolourizing capacity, with a particular preference for the recalcitrant phenothiazine dye class (Azure B, Methylene Blue and Toluidene Blue O). CONCLUSIONS Bacillus sp. LD003 was selected as a promising source of novel types of ligninolytic enzymes. Our observations suggested that lignin mineralization and depolymerization are separate events which place additional challenges on the screening of ligninolytic microorganisms for specific ligninolytic enzymes.
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397
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Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes. PLoS One 2011; 6:e25724. [PMID: 22022440 PMCID: PMC3192119 DOI: 10.1371/journal.pone.0025724] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/09/2011] [Indexed: 11/19/2022] Open
Abstract
Fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. Although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within Bacteria. In this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and four metagenomic datasets, using the custom profile Hidden Markov Models for two- and three-domain laccases. More than 1,200 putative genes for laccase-like enzymes were retrieved from chromosomes and plasmids of diverse bacteria. In 76% of the genes, signal peptides were predicted, indicating that these bacterial laccases may be exported from the cytoplasm, which contrasts with the current belief. Moreover, several examples of putatively horizontally transferred bacterial laccase genes were described. Many metagenomic sequences encoding fragments of laccase-like enzymes could not be phylogenetically assigned, indicating considerable novelty. Laccase-like genes were also found in anaerobic bacteria, autotrophs and alkaliphiles, thus opening new hypotheses regarding their ecological functions. Bacteria identified as carrying laccase genes represent potential sources for future biotechnological applications.
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398
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Abstract
Aromatic compounds are both common growth substrates for microorganisms and prominent environmental pollutants. The crucial step in their degradation is overcoming the resonance energy that stabilizes the ring structure. The classical strategy for degradation comprises an attack by oxygenases that hydroxylate and finally cleave the ring with the help of activated molecular oxygen. Here, we describe three alternative strategies used by microorganisms to degrade aromatic compounds. All three of these methods involve the use of CoA thioesters and ring cleavage by hydrolysis. However, these strategies are based on different ring activation mechanisms that consist of either formation of a non-aromatic ring-epoxide under oxic conditions, or reduction of the aromatic ring under anoxic conditions using one of two completely different systems.
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399
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Bugg TDH, Ahmad M, Hardiman EM, Rahmanpour R. Pathways for degradation of lignin in bacteria and fungi. Nat Prod Rep 2011; 28:1883-96. [PMID: 21918777 DOI: 10.1039/c1np00042j] [Citation(s) in RCA: 455] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lignin is a heterogeneous aromatic polymer found as 10-35% of lignocellulose, found in plant cell walls. The bio-conversion of plant lignocellulose to glucose is an important part of second generation biofuel production, but the resistance of lignin to breakdown is a major obstacle in this process, hence there is considerable interest in the microbial breakdown of lignin. White-rot fungi are known to break down lignin with the aid of extracellular peroxidase and laccase enzymes. There are also reports of bacteria that can degrade lignin, and recent work indicates that bacterial lignin breakdown may be more significant than previously thought. The review will discuss the enzymes for lignin breakdown in fungi and bacteria, and the catabolic pathways for breakdown of the β-aryl ether, biphenyl and other components of lignin in bacteria and fungi. The review will also discuss small molecule phenolic breakdown products from lignin that have been identified from lignin-degrading microbes, and includes a bioinformatic analysis of the occurrence of known lignin-degradation pathways in Gram-positive and Gram-negative bacteria.
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DeAngelis KM, Allgaier M, Chavarria Y, Fortney JL, Hugenholtz P, Simmons B, Sublette K, Silver WL, Hazen TC. Characterization of trapped lignin-degrading microbes in tropical forest soil. PLoS One 2011; 6:e19306. [PMID: 21559391 PMCID: PMC3084812 DOI: 10.1371/journal.pone.0019306] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 04/01/2011] [Indexed: 02/01/2023] Open
Abstract
Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.
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Affiliation(s)
- Kristen M DeAngelis
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National Lab, Berkeley, California, United States of America.
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