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Garcia CA, Gardner JG. RNAseq analysis of Cellvibrio japonicus during starch utilization differentiates between genes encoding carbohydrate active enzymes controlled by substrate detection or growth rate. Microbiol Spectr 2023; 11:e0245723. [PMID: 37800973 PMCID: PMC10714805 DOI: 10.1128/spectrum.02457-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/22/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Understanding the bacterial metabolism of starch is important as this polysaccharide is a ubiquitous ingredient in foods, supplements, and medicines, all of which influence gut microbiome composition and health. Our RNAseq and growth data set provides a valuable resource to those who want to better understand the regulation of starch utilization in Gram-negative bacteria. These data are also useful as they provide an example of how to approach studying a starch-utilizing bacterium that has many putative amylases by coupling transcriptomic data with growth assays to overcome the potential challenges of functional redundancy. The RNAseq data can also be used as a part of larger meta-analyses to compare how C. japonicus regulates carbohydrate active enzymes, or how this bacterium compares to gut microbiome constituents in terms of starch utilization potential.
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Affiliation(s)
- Cecelia A. Garcia
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Jeffrey G. Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
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Zegeye EK, Sadler NC, Lomas GX, Attah IK, Jansson JK, Hofmockel KS, Anderton CR, Wright AT. Activity-Based Protein Profiling of Chitin Catabolism. Chembiochem 2020; 22:717-723. [PMID: 33049124 DOI: 10.1002/cbic.202000616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/12/2020] [Indexed: 01/09/2023]
Abstract
The microbial catabolism of chitin, an abundant and ubiquitous environmental organic polymer, is a fundamental cog in terrestrial and aquatic carbon and nitrogen cycles. Despite the importance of this critical bio-geochemical function, there is a limited understanding of the synergy between the various hydrolytic and accessory enzymes involved in chitin catabolism. To address this deficit, we synthesized activity-based probes (ABPs) designed to target active chitinolytic enzymes by modifying the chitin subunits N-acetyl glucosamine and chitotriose. The ABPs were used to determine the active complement of chitinolytic enzymes produced over time by the soil bacterium Cellvibrio japonicus treated with various C substrates. We demonstrate the utility of these ABPs in determining the synergy between various enzymes involved in chitin catabolism. The strategy can be used to gain molecular-level insights that can be used to better understand microbial roles in soil bio-geochemical cycling in the face of a changing climate.
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Affiliation(s)
- Elias K Zegeye
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, WA 99164, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Natalie C Sadler
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Gerard X Lomas
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Isaac K Attah
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Kirsten S Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
- Department of Ecology, Evolution and Organismal Biology Iowa State University, 251 Bessey Hall, Ames, Iowa (USA) 50011
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Aaron T Wright
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, WA 99164, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
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Gardner JG. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus. World J Microbiol Biotechnol 2016; 32:121. [PMID: 27263016 DOI: 10.1007/s11274-016-2068-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 04/07/2016] [Indexed: 01/10/2023]
Abstract
Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.
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Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
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Xie Z, Lin W, Luo J. Promotion of microalgal growth by co-culturing with Cellvibrio pealriver using xylan as feedstock. Bioresour Technol 2016; 200:1050-1054. [PMID: 26508433 DOI: 10.1016/j.biortech.2015.10.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 10/15/2015] [Accepted: 10/16/2015] [Indexed: 06/05/2023]
Abstract
In this work, a Cellvibrio pealriver-microalga co-cultivation mode was used to promote the growths of four microalgae by using xylan as feedstock. After 12days of cultivation, the biomass concentrations of Chlorella sacchrarophila, Chlorella pyrenoidosa and Chlamydomonas reinhardtii in co-cultivation were equal to those in mixotrophic growth on glucose, and the Dunaliella was about 1.6-fold higher than that on glucose. The comparative transcriptomes analysis demonstrated that the xylose and xylan hydrolysates were catalyzed to some active substrates by C. pealriver via some functional enzymes; these active substrates are possibly responsible for the promotion of microalgal growth. This C. pealriver-microalga co-cultivation mode is a potential method to produce low-cost microalgal biodiesel by using hemicellulose as feedstock.
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Affiliation(s)
- Zhangzhang Xie
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, PR China
| | - Weitie Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jianfei Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, PR China.
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Centeno MSJ, Guerreiro CIPD, Dias FMV, Morland C, Tailford LE, Goyal A, Prates JAM, Ferreira LMA, Caldeira RMH, Mongodin EF, Nelson KE, Gilbert HJ, Fontes CMGA. Galactomannan hydrolysis and mannose metabolism in Cellvibrio mixtus. FEMS Microbiol Lett 2006; 261:123-32. [PMID: 16842369 DOI: 10.1111/j.1574-6968.2006.00342.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Galactomannan hydrolysis results from the concerted action of microbial endo-mannanases, manosidases and alpha-galactosidases and is a mechanism of intrinsic biological importance. Here we report the identification of a gene cluster in the aerobic soil bacterium Cellvibrio mixtus encoding enzymes involved in the degradation of this polymeric substrate. The family 27 alpha-galactosidase, termed CmAga27A, preferentially hydrolyse galactose containing polysaccharides. In addition, we have characterized an enzyme with epimerase activity, which might be responsible for the conversion of mannose into glucose. The role of the identified enzymes in the hydrolysis of galactomannan by aerobic bacteria is discussed.
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Affiliation(s)
- Maria S J Centeno
- CIISA - Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Lisboa, Portugal
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Nakajima-Kambe T, Okada N, Takeda M, Akutsu-Shigeno Y, Matsumura M, Nomura N, Uchiyama H. Screening of novel cellulose-degrading bacterium and its application to denitrification of groundwater. J Biosci Bioeng 2005; 99:429-33. [PMID: 16233813 DOI: 10.1263/jbb.99.429] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2004] [Accepted: 01/27/2005] [Indexed: 11/17/2022]
Abstract
To establish an environmentally friendly groundwater bioremediation process using a cellulose carrier combined with cellulose-utilizing, denitrifying microorganisms, a novel psychrophilic bacterium, designated CL-5, which can degrade a commercial-based cellulose carrier as the sole carbon source, was screened. Since the denitrification capability of CL-5 is low, complex microbial systems were constructed together with other denitrifying bacteria designated NR-1 and NR-2 that were also isolated from soil. The nitrate-reducing activities of mixed cultures were much higher than those of the pure cultures of CL-5, NR-1 and NR-2. The highest N(2)O and N(2) formation activities were observed in the mixed culture of CL-5+NR-2.
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Yamaguchi A, Tada T, Nakaniwa T, Kitatani T, Takao M, Sakai T, Nishimura K. Crystallization and preliminary X-ray diffraction analysis of a thermostable endo-1,5-α-L-arabinanase fromBacillus thermodenitrificansTS-3. Acta Crystallogr D Biol Crystallogr 2004; 60:1149-51. [PMID: 15159584 DOI: 10.1107/s0907444904008534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2004] [Accepted: 04/09/2004] [Indexed: 11/10/2022]
Abstract
A thermostable endo-1,5-alpha-L-arabinanase ABN-TS from Bacillus thermodenitrificans TS-3 with a molecular weight of 35 kDa was crystallized by the hanging-drop vapour-diffusion method using sodium citrate as a precipitant. The crystals were loop-mounted in a cryoprotectant solution containing 28%(w/v) sucrose and 1 M sodium citrate pH 6.0 and flash-cooled. Sucrose was selected as the most suitable cryoprotectant. The crystal belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 40.3, b = 77.8, c = 89.7 angstroms. The calculated VM based on one molecule per asymmetric unit was 2.0 angstroms3 Da(-1). A complete data set from a frozen crystal was collected to 1.9 angstroms resolution using synchrotron radiation at SPring-8. A molecular-replacement solution was obtained using the structure of alpha-arabinanase 43A from Cellvibrio japonicus.
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Affiliation(s)
- Asako Yamaguchi
- Research Institute for Advanced Science and Technology, Osaka Prefecture University, Sakai, Osaka 599-8570, Japan.
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Henshaw JL, Bolam DN, Pires VMR, Czjzek M, Henrissat B, Ferreira LMA, Fontes CMGA, Gilbert HJ. The family 6 carbohydrate binding module CmCBM6-2 contains two ligand-binding sites with distinct specificities. J Biol Chem 2004; 279:21552-9. [PMID: 15004011 DOI: 10.1074/jbc.m401620200] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The microbial degradation of the plant cell wall is an important biological process, representing a major component of the carbon cycle. Enzymes that mediate the hydrolysis of this composite structure are modular proteins that contain non-catalytic carbohydrate binding modules (CBMs) that enhance catalytic activity. CBMs are grouped into sequence-based families, and in a previous study we showed that a family 6 CBM (CBM6) that interacts with xylan contains two potential ligand binding clefts, designated cleft A and cleft B. Mutagenesis and NMR studies showed that only cleft A in this protein binds to xylan. Family 6 CBMs bind to a range of polysaccharides, and it was proposed that the variation in ligand specificity observed in these proteins reflects the specific cleft that interacts with the target carbohydrate. Here the biochemical properties of the C-terminal cellulose binding CBM6 (CmCBM6-2) from Cellvibrio mixtus endoglucanase 5A were investigated. The CBM binds to the beta1,4-beta1,3-mixed linked glucans lichenan and barley beta-glucan, cello-oligosaccharides, insoluble forms of cellulose, the beta1,3-glucan laminarin, and xylooligosaccharides. Mutagenesis studies, informed by the crystal structure of the protein (presented in the accompanying paper, Pires, V. M. R., Henshaw, J. L., Prates, J. A. M., Bolam, D., Ferreira, L. M. A. Fontes, C. M. G. A., Henrissat, B., Planas, A., Gilbert, H. J., Czjzek, M. (2004) J. Biol. Chem. 279, 21560-21568), show that both cleft A and B can accommodate cello-oligosaccharides and laminarin displays a preference for cleft A, whereas xylooligosaccharides exhibit absolute specificity for this site, and the beta1,4,-beta1,3-mixed linked glucans interact only with cleft B. The binding of CmCBM6-2 to insoluble cellulose involves synergistic interactions between cleft A and cleft B. These data show that CmCBM6-2 contains two binding sites that display differences in ligand specificity, supporting the view that distinct binding clefts with different specificities can contribute to the variation in ligand recognition displayed by family 6 CBMs. This is in sharp contrast to other CBM families, where variation in ligand binding is a result of changes in the topology of a single carbohydrate-binding site.
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Affiliation(s)
- Joanna L Henshaw
- School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, United Kingdom
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Modelli A, Rondinelli G, Scandola M, Mergaert J, Cnockaert MC. Biodegradation of Chemically Modified Flax Fibers in Soil and in Vitro with Selected Bacteria. Biomacromolecules 2004; 5:596-602. [PMID: 15003026 DOI: 10.1021/bm0344203] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The extent and rate of degradation of flax (Linum usitatissimum) fibers, both in the native state and after surface chemical modification (acetylation or poly(ethylene glycol), PEG, grafting), was investigated under laboratory conditions in two different biodegrading environments. Degradation of the fibers under aerobic conditions by the action of the microorganisms present in soil is assessed with the ASTM 5988-96 method by monitoring carbon dioxide evolution. In vitro biodegradation experiments were carried out by exposing the fibers to a pure culture of Cellvibrio fibrovorans bacteria and measuring the mass loss as a function of time. Despite the complexity of the system, the results of degradation in soil were satisfactorily reproducible, although the absolute rates were found to change in different experiments using the same soil. The degradation rate of acetylated fibers in soil nearly equals that of unmodified fibers, whereas in the pure culture, acetylated fibers biodegrade slower than native fibers. The opposite happens with the PEG-grafted fibers, which degrade slower than unmodified flax in soil and at a comparable rate upon in vitro exposure to the bacterial culture. The different biodegradation kinetics observed in the two biodegrading environments were attributed to differences of biocenoses, abiotic factors, and biodegradation assessing methods. Nevertheless, the final extent of biodegradation was the same for modified and unmodified fibers both in soil and in the pure culture, showing that the surface chemical modifications applied do not significantly affect biodegradability of the flax fibers.
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Affiliation(s)
- Alberto Modelli
- Dipartimento di Chimica G Ciamician, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
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Humphry DR, Black GW, Cummings SP. Reclassification of 'Pseudomonas fluorescens subsp. cellulosa' NCIMB 10462 (Ueda et al. 1952) as Cellvibrio japonicus sp. nov. and revival of Cellvibrio vulgaris sp. nov., nom. rev. and Cellvibrio fulvus sp. nov., nom. rev. Int J Syst Evol Microbiol 2003; 53:393-400. [PMID: 12710603 DOI: 10.1099/ijs.0.02271-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
'Pseudomonas fluorescens subsp. cellulosa' NCIMB 10462 has been demonstrated by a polyphasic taxonomic approach to be a member of the genus Cellvibrio. 16S rDNA sequence analysis suggests that this is the only genus that could accept this specimen. The sequence is 95.5% similar to that of Cellvibrio mixtus subsp. mixtus ACM 2601T (the type strain of the type species of the genus), which is its closest relation. The genomic DNA G + C content was determined to be 53.3 mol%, which is similar to the values obtained for the validly described Cellvibrio species. DNA-DNA hybridization experiments have shown that strain NCIMB 10462T (= NCDO 2697T) represents a novel species; therefore, it is proposed that it be designated as the type strain of the novel species Cellvibrio japonicus sp. nov. This study also used 16S rDNA analysis, DNA-DNA hybridization experiments and phenotypic testing to revive the species Cellvibrio vulgaris sp. nov., nom. rev. and Cellvibrio fulvus sp. nov., nom. rev. C. vulgaris NCIMB 8633T (=LMG 2848T) and C. fulvus NCIMB 8634T (=LMG 2847T) are the proposed type strains.
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Affiliation(s)
- David R Humphry
- The School of Health, Natural and Social Sciences, University of Sunderland, Sunderland SR1 3SD, UK
| | - Gary W Black
- School of Applied Sciences, Northumbria University, Ellison Building, Newcastle upon Tyne NE1 8ST, UK
| | - Stephen P Cummings
- The School of Health, Natural and Social Sciences, University of Sunderland, Sunderland SR1 3SD, UK
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Frisoni G, Baiardo M, Scandola M, Lednická D, Cnockaert MC, Mergaert J, Swings J. Natural cellulose fibers: heterogeneous acetylation kinetics and biodegradation behavior. Biomacromolecules 2003; 2:476-82. [PMID: 11749209 DOI: 10.1021/bm0056409] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Steam-exploded fibers from flax (Linum usitatissimum) are heterogeneously acetylated using acetic anhydride and sulfuric acid as catalyst, with the aim to modify the surface properties without changing fiber structure and morphology. The acetylation reaction follows first-order kinetics up to a reaction time that depends on catalyst concentration (15 h when using 0.4 vol % of H(2)SO(4) or 50 h with 0.1 vol %). The fibers undergo no structural and/or morphological changes under either reaction condition. On the contrary, surface damage and structural modifications appear after longer reaction times, when the reaction kinetics change. The extent of biodegradation of acetylated fibers, evaluated from the weight percent remaining after 13 days of exposure to previously isolated cellulolytic bacteria Cellvibrio sp., decreases with increasing acetylation degree. After biodegradation the fibers show a higher acetyl content than before the experiment, indicating that the bacteria preferentially biodegrade unsubstituted cellulose, though also acetylated chains are cleaved. Biodegradable acetylated cellulose fibers with modified surface chemistry and unchanged structure are obtained for applications as polymer composite reinforcements.
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Affiliation(s)
- G Frisoni
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
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STORVICK WO, KING KW. The complexity and mode of action of the cellulase system of Cellvibrio gilvus. J Biol Chem 1960; 235:303-7. [PMID: 13834997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
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BORTELS H. [Significance of trace elements for cell vibrio and Cytophaga species types]. Arch Mikrobiol 1956; 25:225-46. [PMID: 13395442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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