1
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Maeda T, Kotani H, Furusawa C. Morphological change of coiled bacterium Spirosoma linguale with acquisition of β-lactam resistance. Sci Rep 2021; 11:13278. [PMID: 34168257 PMCID: PMC8225782 DOI: 10.1038/s41598-021-92787-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/14/2021] [Indexed: 11/24/2022] Open
Abstract
Spirosoma linguale is a gram-negative, coiled bacterium belonging to the family Cytophagaceae. Its coiled morphology is unique in contrast to closely related bacteria belonging to the genus Spirosoma, which have a short, rod-shaped morphology. The mechanisms that generate unique cell morphology are still enigmatic. In this study, using the Spirosoma linguale ATCC33905 strain, we isolated β-lactam (cefoperazone and amoxicillin)-resistant clones. These clones showed two different cell morphological changes: relatively loosely curved cells or small, horseshoe-shaped cells. Whole-genome resequencing analysis revealed the genetic determinants of β-lactam resistance and changes in cell morphology. The loose-curved clones commonly had mutations in Slin_5958 genes encoding glutamyl-tRNA amidotransferase B subunit, whereas the small, horseshoe-shaped clones commonly had mutations in either Slin_5165 or Slin_5509 encoding pyruvate dehydrogenase (PDH) components. Two clones, CFP1ESL11 and CFL5ESL4, which carried only one mutation in Slin_5958, showed almost perfectly straight, rod-shaped cells in the presence of amoxicillin. This result suggests that penicillin-binding proteins targeted by amoxicillin play an important role in the formation of a coiled morphology in this bacterium. In contrast, supplementation with acetate did not rescue the growth defect and abnormal cell size of the CFP5ESL9 strain, which carried only one mutation in Slin_5509. These results suggest that PDH is involved in cell-size maintenance in this bacterium.
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Affiliation(s)
- Tomoya Maeda
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan.
| | - Hazuki Kotani
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Chikara Furusawa
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Department of Physics, The University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan
- Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan
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2
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Kang H, Cha I, Kim H, Joh K. Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. isolated from soil and tree bark, respectively. Int J Syst Evol Microbiol 2020; 70:5355-5362. [DOI: 10.1099/ijsem.0.004418] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Two novel strains (HMF3257T and HMF4905T), isolated from freshwater and bark samples, were investigated to determine their relationships within and between species of the genus
Spirosoma
by using a polyphasic approach. They were aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria. The major fatty acids (>10%) in both strains were identified as summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and C16 : 1
ω5c, while strains HMF3257T and HMF4905T contained a moderately high amount of C16 : 0 and iso-C15 : 0, respectively. The predominant respiratory quinone was MK-7 for both strains. In addition to phosphatidylethanolamine and one unidentified glycolipid, the polar lipid profile of strain HMF3257T consisted of three unidentified aminophospholipids, one unidentified aminolipid and two unidentified polar lipids, and that of strain HMF4905T consisted of one unidentified aminophospholipid, two unidentified aminolipids and three unidentified polar lipids. The DNA G+C contents of strains HMF3257T and HMF4905T were 47.2 and 46.4 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains HMF3257T and HMF4905T are closely related to
Spirosoma migulaei
15J9-8T (97.0 % sequence similarity), while sharing 97.4 % sequence similarity with each other. The average nucleotide identity value between strains HMF3257T and HMF4905T was 81.1 %, and the digital DNA–DNA hybridization value between these two strains was 24.4 %. Based on the above data, strains HMF3257T and HMF4905T represent two novel members within the genus
Spirosoma
, for which the names Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. are proposed, respectively. The type strain of S. telluris is HMF3257T (=KCTC 62463T=NBRC 112670T) and type strain of S. arboris is HMF4905T (=KCTC 72779T=NBRC 114270T).
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Affiliation(s)
- Heeyoung Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Inseong Cha
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
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3
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Ambika Manirajan B, Suarez C, Ratering S, Rusch V, Geissler-Plaum R, Cardinale M, Schnell S. Spirosoma pollinicola sp. nov., isolated from pollen of common hazel (Corylus avellana L.). Int J Syst Evol Microbiol 2018; 68:3248-3254. [DOI: 10.1099/ijsem.0.002973] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Binoy Ambika Manirajan
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Christian Suarez
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Stefan Ratering
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Volker Rusch
- 2Institute for Integrative Biology, Old Herborn University Foundation, Herborn, Germany
| | - Rita Geissler-Plaum
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Massimiliano Cardinale
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Sylvia Schnell
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
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4
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Li W, Ten LN, Lee SY, Kang IK, Jung HY. Spirosoma horti sp. nov., isolated from apple orchard soil. Int J Syst Evol Microbiol 2018; 68:930-935. [DOI: 10.1099/ijsem.0.002614] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Weilan Li
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Leonid N. Ten
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seung-Yeol Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - In-Kyu Kang
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hee-Young Jung
- Institute of Plant Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
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5
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Spirosoma pomorum sp. nov., isolated from apple orchard soil. J Microbiol 2018; 56:90-96. [PMID: 29392558 DOI: 10.1007/s12275-018-7430-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 12/29/2017] [Accepted: 01/04/2018] [Indexed: 01/06/2023]
Abstract
A Gram-negative, motile, rod-shaped, aerobic bacterial strain, designated S7-2-11T, was isolated from apple orchard soil from Gyeongsangnam-do Province, Republic of Korea, and was characterized taxonomically using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain S7-2-11T belongs to the family Cytophagaceae in phylum Bacteroidetes, and is closely related to Spirosoma luteolum 16F6ET (94.2% identity), Spirosoma knui 15J8-12T (92.7%), and Spirosoma linguale DSM 74T (91.0%). The G + C content of the genomic DNA of strain S7-2-11T was 49.8 mol%. Strain S7-2-11T contained summed feature 3 (C16:1 ω7c/C16:1 ω6c; 35.1%), C16:1 ω5c (22.4%), C15:0 iso (13.9%), and C17:0 iso 3-OH (10.6%) as major cellular fatty acids, and MK-7 as the predominant respiratory quinone. The main polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid, and two unidentified polar lipids. Phenotypic and chemotaxonomic data supported the affiliation of strain S7-2-11T with the genus Spirosoma. The results of physiological and biochemical tests showed the genotypic and phenotypic differentiation of the isolate from recognized Spirosoma species. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain S7-2-11T represents a novel species of the genus Spirosoma, for which the name Spirosoma pomorum sp. nov. is proposed. The type strain is S7-2-11T (= KCTC 52726T = JCM 32130T).
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6
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Li W, Lee SY, Kang IK, Ten LN, Jung HY. Spirosoma agri sp. nov., Isolated from Apple Orchard Soil. Curr Microbiol 2018; 75:694-700. [DOI: 10.1007/s00284-018-1434-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/05/2018] [Indexed: 10/18/2022]
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7
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Arnling Bååth J, Mazurkewich S, Knudsen RM, Poulsen JCN, Olsson L, Lo Leggio L, Larsbrink J. Biochemical and structural features of diverse bacterial glucuronoyl esterases facilitating recalcitrant biomass conversion. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:213. [PMID: 30083226 PMCID: PMC6069808 DOI: 10.1186/s13068-018-1213-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/23/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Lignocellulose is highly recalcitrant to enzymatic deconstruction, where the recalcitrance primarily results from chemical linkages between lignin and carbohydrates. Glucuronoyl esterases (GEs) from carbohydrate esterase family 15 (CE15) have been suggested to play key roles in reducing lignocellulose recalcitrance by cleaving covalent ester bonds found between lignin and glucuronoxylan. However, only a limited number of GEs have been biochemically characterized and structurally determined to date, limiting our understanding of these enzymes and their potential exploration. RESULTS Ten CE15 enzymes from three bacterial species, sharing as little as 20% sequence identity, were characterized on a range of model substrates; two protein structures were solved, and insights into their regulation and biological roles were gained through gene expression analysis and enzymatic assays on complex biomass. Several enzymes with higher catalytic efficiencies on a wider range of model substrates than previously characterized fungal GEs were identified. Similarities and differences regarding substrate specificity between the investigated GEs were observed and putatively linked to their positioning in the CE15 phylogenetic tree. The bacterial GEs were able to utilize substrates lacking 4-OH methyl substitutions, known to be important for fungal enzymes. In addition, certain bacterial GEs were able to efficiently cleave esters of galacturonate, a functionality not previously described within the family. The two solved structures revealed similar overall folds to known structures, but also indicated active site regions allowing for more promiscuous substrate specificities. The gene expression analysis demonstrated that bacterial GE-encoding genes were differentially expressed as response to different carbon sources. Further, improved enzymatic saccharification of milled corn cob by a commercial lignocellulolytic enzyme cocktail when supplemented with GEs showcased their synergistic potential with other enzyme types on native biomass. CONCLUSIONS Bacterial GEs exhibit much larger diversity than fungal counterparts. In this study, we significantly expanded the existing knowledge on CE15 with the in-depth characterization of ten bacterial GEs broadly spanning the phylogenetic tree, and also presented two novel enzyme structures. Variations in transcriptional responses of CE15-encoding genes under different growth conditions suggest nonredundant functions for enzymes found in species with multiple CE15 genes and further illuminate the importance of GEs in native lignin-carbohydrate disassembly.
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Affiliation(s)
- Jenny Arnling Bååth
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Scott Mazurkewich
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | | | - Lisbeth Olsson
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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8
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Okiria J, Ten LN, Park SJ, Lee SY, Lee DH, Kang IK, Lee DS, Jung HY. Spirosoma migulaei sp. nov., isolated from soil. J Microbiol 2017; 55:927-932. [DOI: 10.1007/s12275-017-7377-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 12/12/2022]
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9
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Ten LN, Okiria J, Lee JJ, Lee SY, Park S, Lee DS, Kang IK, Kim MK, Jung HY. Spirosoma terrae sp. nov., Isolated from Soil from Jeju Island, Korea. Curr Microbiol 2017; 75:492-498. [DOI: 10.1007/s00284-017-1408-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/29/2017] [Indexed: 12/11/2022]
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10
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Ten LN, Okiria J, Lee JJ, Lee SY, Kang IK, Lee DS, Jung HY. Spirosoma koreense sp. nov., a species of the family Cytophagaceae isolated from beach soil. Int J Syst Evol Microbiol 2017; 67:5198-5204. [DOI: 10.1099/ijsem.0.002440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Leonid N. Ten
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Joseph Okiria
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jae-Jin Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seung-Yeol Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - In-Kyu Kang
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Dae Sung Lee
- Department of Environmental Engineering, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hee-Young Jung
- Institute of Plant Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
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11
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Okiria J, Ten LN, Lee JJ, Lee SY, Cho YJ, Kim MK, Jung HY. Spirosoma litoris sp. nov., a bacterium isolated from beach soil. Int J Syst Evol Microbiol 2017; 67:4986-4991. [DOI: 10.1099/ijsem.0.002394] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Joseph Okiria
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Leonid N. Ten
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jae-Jin Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seung-Yeol Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Young-Je Cho
- School of Food Science and Biotechnology/Food and Bio-Industry Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio and Environmental Technology, Seoul Women’s University, Seoul 01797, Republic of Korea
| | - Hee-Young Jung
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
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12
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Spirosoma jeollabukense sp. nov., isolated from soil. Arch Microbiol 2017; 200:431-438. [DOI: 10.1007/s00203-017-1453-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/25/2017] [Accepted: 11/13/2017] [Indexed: 02/06/2023]
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13
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Weilan L, Lee JJ, Lee SY, Park S, Ten LN, Jung HY. Spirosoma humi sp. nov., Isolated from Soil in South Korea. Curr Microbiol 2017; 75:328-335. [DOI: 10.1007/s00284-017-1384-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/28/2017] [Indexed: 01/03/2023]
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14
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Elderiny N, Lee SY, Park S, Kang IK, Kim MK, Lee DS, Ten LN, Jung HY. Spirosoma flavus sp. nov., a novel bacterium from soil of Jeju Island. J Microbiol 2017; 55:850-855. [PMID: 29076067 DOI: 10.1007/s12275-017-7360-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/28/2017] [Accepted: 10/03/2017] [Indexed: 10/18/2022]
Abstract
A novel, Gram-staining negative, yellow pigmented bacterial strain, designated 15J11-2T, was isolated from soil sample on Jeju Island, Republic of Korea. The strain was subjected to a taxonomic study using a polyphasic approach. The strain was able to grow at temperature range from 10°C to 30°C, pH 7-8, and in presence of 0-1% (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain 15J11-2T belongs to the genus Spirosoma and levels of 16S rRNA gene sequence similarity ranged from 91.5% to 89.8%. The genomic DNA G + C content of strain 15J11-2T was 46.0 mol%. The isolate contained phosphatidylethanolamine and an unidentified aminophospholipid as the main polar lipids, menaquinone MK-7 as the predominant respiratory quinone, and summed feature 3 (C16:1 ω6c/C16:1 ω7c; 39.4%), C16:1 ω5c (27.1%), and C16:0 (13.0%) as the major fatty acids, which supported the affiliation of strain 15J11-2T to the genus Spirosoma. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 15J11-2T from recognized Spirosoma species. On the basis of its phenotypic properties, genotypic distinctiveness, chemotaxonomic features, strain 15J11-2T represents a novel species of the genus Spirosoma, for which the name Spirosoma flavus sp. nov. is proposed. The type strain is 15J11-2T (= KCTC 52026T = JCM 31998T).
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Affiliation(s)
- Nabil Elderiny
- College of Agricultural and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung-Yeol Lee
- College of Agricultural and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sangkyu Park
- College of Agricultural and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - In-Kyu Kang
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio and Environmental Technology, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Dae Sung Lee
- Department of Environmental Engineering, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Leonid N Ten
- College of Agricultural and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hee-Young Jung
- College of Agricultural and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea. .,Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.
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15
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Spirosoma lituiforme sp. nov., isolated from soil. J Microbiol 2017; 55:856-861. [DOI: 10.1007/s12275-017-7255-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/27/2017] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
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16
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Spirosoma harenae sp. nov., a Bacterium Isolated from a Sandy Beach. Curr Microbiol 2017; 75:179-185. [DOI: 10.1007/s00284-017-1363-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/06/2017] [Indexed: 11/25/2022]
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17
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Elderiny N, Ten LN, Lee JJ, Lee SY, Park S, Cho YJ, Kim MK, Jung HY. Spirosoma daeguensis sp. nov., isolated from beach soil. J Microbiol 2017; 55:678-683. [DOI: 10.1007/s12275-017-7211-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/24/2017] [Accepted: 07/28/2017] [Indexed: 10/18/2022]
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18
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The unusual cellulose utilization system of the aerobic soil bacterium Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2017; 101:7113-7127. [PMID: 28849247 DOI: 10.1007/s00253-017-8467-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 08/05/2017] [Indexed: 10/19/2022]
Abstract
Cellulolytic microorganisms play important roles in global carbon cycling and have evolved diverse strategies to digest cellulose. Some are 'generous,' releasing soluble sugars from cellulose extracellularly to feed both themselves and their neighbors. The gliding soil bacterium Cytophaga hutchinsonii exhibits a more 'selfish' strategy. It digests crystalline cellulose using cell-associated cellulases and releases little soluble sugar outside of the cell. The mechanism of C. hutchinsonii cellulose utilization is still poorly understood. In this review, we discuss novel aspects of the C. hutchinsonii cellulolytic system. Recently developed genetic manipulation tools allowed the identification of proteins involved in C. hutchinsonii cellulose utilization. These include periplasmic and cell-surface endoglucanases and novel cellulose-binding proteins. The recently discovered type IX secretion system is needed for cellulose utilization and appears to deliver some of the cellulolytic enzymes and other proteins to the cell surface. The requirement for periplasmic endoglucanases for cellulose utilization is unusual and suggests that cello-oligomers must be imported across the outer membrane before being further digested. Cellobiohydrolases or other predicted processive cellulases that play important roles in many other cellulolytic bacteria appear to be absent in C. hutchinsonii. Cells of C. hutchinsonii attach to and glide along cellulose fibers, which may allow them to find sites most amenable to attack. A model of C. hutchinsonii cellulose utilization summarizing recent progress is proposed.
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19
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Lee JJ, Elderiny N, Lee SY, Lee DS, Kim MK, Ten LN, Jung HY. Spirosoma gilvum sp. nov., Isolated from Beach Soil. Curr Microbiol 2017; 74:1425-1431. [DOI: 10.1007/s00284-017-1336-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/10/2017] [Indexed: 12/01/2022]
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20
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Spirosoma metallum sp. nov., isolated from an automobile air conditioning system. Arch Microbiol 2017; 200:91-96. [PMID: 28799031 DOI: 10.1007/s00203-017-1424-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 10/19/2022]
Abstract
A Gram-stain-negative and yellow-pigmented bacterial strain, designated TX0653T, was isolated from an automobile evaporator core collected in Korea. The cells were aerobic and rod-shaped. The strain grew at 10-28 °C (optimum, 25 °C), at pH 6.0-7.5 (optimum, 6.5), and in the presence of 0-1% (w/v) NaCl (optimum, 0%). Phylogenetically, the strain was related to members of the genus Spirosoma (95.1-90.8% 16S rRNA sequence similarity) and distantly related to Spirosoma pulveris JSH5-14T (95.1%), Spirosoma fluviale MSd3T (95.0%), Spirosoma endophyticum DSM 26130T (94.8%), and Spirosoma linguale DSM 74T (94.6%). The major fatty acids of the strain were summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C16:1 ω5c, iso-C15:0, iso-C17:0 3-OH, and C16:0. MK-7 was identified as the predominant menaquinone. The polar lipids profile indicated the presence of one phosphatidylethanolamine, one unidentified aminolipid, one unidentified aminophospholipid, two unidentified phospholipids, and three unidentified lipids. On the basis of the phenotypic, genotypic, and chemotaxonomic characteristics, strain TX0653T represents a novel species in the genus Spirosoma, for which the name Spirosoma metallum sp. nov. (= KACC 19278T = NBRC 112495T) is proposed.
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Lee JJ, Lee YH, Park SJ, Lee SY, Kim BO, Ten LN, Kim MK, Jung HY. Spirosoma knui sp. nov., a radiation-resistant bacterium isolated from the Han River. Int J Syst Evol Microbiol 2017; 67:1359-1365. [DOI: 10.1099/ijsem.0.001817] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jae-Jin Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yeon-Hee Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Su-Jin Park
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seung-Yeol Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Byung-Oh Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Leonid N Ten
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 01797, Republic of Korea
| | - Hee-Young Jung
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
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22
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Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Göker M. Genome-Based Taxonomic Classification of Bacteroidetes. Front Microbiol 2016; 7:2003. [PMID: 28066339 PMCID: PMC5167729 DOI: 10.3389/fmicb.2016.02003] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/30/2016] [Indexed: 01/15/2023] Open
Abstract
The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.
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Affiliation(s)
- Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Supratim Mukherjee
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Natalia N. Ivanova
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Nikos C. Kyrpides
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
- Department of Biological Sciences, Faculty of Science, King Abdulaziz UniversityJeddah, Saudi Arabia
| | | | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
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23
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Jiang C, Caccamo PD, Brun YV. Mechanisms of bacterial morphogenesis: evolutionary cell biology approaches provide new insights. Bioessays 2015; 37:413-25. [PMID: 25664446 DOI: 10.1002/bies.201400098] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
How Darwin's "endless forms most beautiful" have evolved remains one of the most exciting questions in biology. The significant variety of bacterial shapes is most likely due to the specific advantages they confer with respect to the diverse environments they occupy. While our understanding of the mechanisms generating relatively simple shapes has improved tremendously in the last few years, the molecular mechanisms underlying the generation of complex shapes and the evolution of shape diversity are largely unknown. The emerging field of bacterial evolutionary cell biology provides a novel strategy to answer this question in a comparative phylogenetic framework. This relatively novel approach provides hypotheses and insights into cell biological mechanisms, such as morphogenesis, and their evolution that would have been difficult to obtain by studying only model organisms. We discuss the necessary steps, challenges, and impact of integrating "evolutionary thinking" into bacterial cell biology in the genomic era.
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Affiliation(s)
- Chao Jiang
- Department of Biology, Indiana University, Bloomington, IN, USA
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24
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Draft Genome Sequence of Cellulose-Digesting Bacterium Sporocytophaga myxococcoides PG-01. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01154-14. [PMID: 25414493 PMCID: PMC4239348 DOI: 10.1128/genomea.01154-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sporocytophaga myxococcoides, a Gram-negative bacterium isolated from soil, is an efficient hydrolyzer of crystalline cellulose. Here, we report its draft genome sequence, which may provide important genetic information regarding the cellulolytic and hemicellulolytic enzymes that contribute to the cellulose-degrading abilities of this bacterium.
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25
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Piao H, Froula J, Du C, Kim TW, Hawley ER, Bauer S, Wang Z, Ivanova N, Clark DS, Klenk HP, Hess M. Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation. Biotechnol Bioeng 2014; 111:1550-65. [PMID: 24728961 DOI: 10.1002/bit.25250] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 02/21/2014] [Accepted: 03/24/2014] [Indexed: 11/06/2022]
Abstract
Although recent nucleotide sequencing technologies have significantly enhanced our understanding of microbial genomes, the function of ∼35% of genes identified in a genome currently remains unknown. To improve the understanding of microbial genomes and consequently of microbial processes it will be crucial to assign a function to this "genomic dark matter." Due to the urgent need for additional carbohydrate-active enzymes for improved production of transportation fuels from lignocellulosic biomass, we screened the genomes of more than 5,500 microorganisms for hypothetical proteins that are located in the proximity of already known cellulases. We identified, synthesized and expressed a total of 17 putative cellulase genes with insufficient sequence similarity to currently known cellulases to be identified as such using traditional sequence annotation techniques that rely on significant sequence similarity. The recombinant proteins of the newly identified putative cellulases were subjected to enzymatic activity assays to verify their hydrolytic activity towards cellulose and lignocellulosic biomass. Eleven (65%) of the tested enzymes had significant activity towards at least one of the substrates. This high success rate highlights that a gene context-based approach can be used to assign function to genes that are otherwise categorized as "genomic dark matter" and to identify biomass-degrading enzymes that have little sequence similarity to already known cellulases. The ability to assign function to genes that have no related sequence representatives with functional annotation will be important to enhance our understanding of microbial processes and to identify microbial proteins for a wide range of applications.
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Affiliation(s)
- Hailan Piao
- School of Molecular Biosciences, Washington State University, Richland, Washington, 99352; Pacific Northwest National Laboratory, Richland, Washington
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26
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Kodavali PK, Dudkiewicz M, Pikuła S, Pawłowski K. Bioinformatics analysis of bacterial annexins--putative ancestral relatives of eukaryotic annexins. PLoS One 2014; 9:e85428. [PMID: 24454864 PMCID: PMC3894181 DOI: 10.1371/journal.pone.0085428] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 12/03/2013] [Indexed: 11/19/2022] Open
Abstract
Annexins are Ca(2+)-binding, membrane-interacting proteins, widespread among eukaryotes, consisting usually of four structurally similar repeated domains. It is accepted that vertebrate annexins derive from a double genome duplication event. It has been postulated that a single domain annexin, if found, might represent a molecule related to the hypothetical ancestral annexin. The recent discovery of a single-domain annexin in a bacterium, Cytophaga hutchinsonii, apparently confirmed this hypothesis. Here, we present a more complex picture. Using remote sequence similarity detection tools, a survey of bacterial genomes was performed in search of annexin-like proteins. In total, we identified about thirty annexin homologues, including single-domain and multi-domain annexins, in seventeen bacterial species. The thorough search yielded, besides the known annexin homologue from C. hutchinsonii, homologues from the Bacteroidetes/Chlorobi phylum, from Gemmatimonadetes, from beta- and delta-Proteobacteria, and from Actinobacteria. The sequences of bacterial annexins exhibited remote but statistically significant similarity to sequence profiles built of the eukaryotic ones. Some bacterial annexins are equipped with additional, different domains, for example those characteristic for toxins. The variation in bacterial annexin sequences, much wider than that observed in eukaryotes, and different domain architectures suggest that annexins found in bacteria may actually descend from an ancestral bacterial annexin, from which eukaryotic annexins also originate. The hypothesis of an ancient origin of bacterial annexins has to be reconciled with the fact that remarkably few bacterial strains possess annexin genes compared to the thousands of known bacterial genomes and with the patchy, anomalous phylogenetic distribution of bacterial annexins. Thus, a massive annexin gene loss in several bacterial lineages or very divergent evolution would appear a likely explanation. Alternative evolutionary scenarios, involving horizontal gene transfer between bacteria and protozoan eukaryotes, in either direction, appear much less likely. Altogether, current evidence does not allow unequivocal judgement as to the origin of bacterial annexins.
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Affiliation(s)
- Praveen Kumar Kodavali
- Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Małgorzata Dudkiewicz
- Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Sławomir Pikuła
- Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Krzysztof Pawłowski
- Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
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27
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Functional screening of metagenome and genome libraries for detection of novel flavonoid-modifying enzymes. Appl Environ Microbiol 2013; 79:4551-63. [PMID: 23686272 DOI: 10.1128/aem.01077-13] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The functional detection of novel enzymes other than hydrolases from metagenomes is limited since only a very few reliable screening procedures are available that allow the rapid screening of large clone libraries. For the discovery of flavonoid-modifying enzymes in genome and metagenome clone libraries, we have developed a new screening system based on high-performance thin-layer chromatography (HPTLC). This metagenome extract thin-layer chromatography analysis (META) allows the rapid detection of glycosyltransferase (GT) and also other flavonoid-modifying activities. The developed screening method is highly sensitive, and an amount of 4 ng of modified flavonoid molecules can be detected. This novel technology was validated against a control library of 1,920 fosmid clones generated from a single Bacillus cereus isolate and then used to analyze more than 38,000 clones derived from two different metagenomic preparations. Thereby we identified two novel UDP glycosyltransferase (UGT) genes. The metagenome-derived gtfC gene encoded a 52-kDa protein, and the deduced amino acid sequence was weakly similar to sequences of putative UGTs from Fibrisoma and Dyadobacter. GtfC mediated the transfer of different hexose moieties and exhibited high activities on flavones, flavonols, flavanones, and stilbenes and also accepted isoflavones and chalcones. From the control library we identified a novel macroside glycosyltransferase (MGT) with a calculated molecular mass of 46 kDa. The deduced amino acid sequence was highly similar to sequences of MGTs from Bacillus thuringiensis. Recombinant MgtB transferred the sugar residue from UDP-glucose effectively to flavones, flavonols, isoflavones, and flavanones. Moreover, MgtB exhibited high activity on larger flavonoid molecules such as tiliroside.
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Abstract
Fibrisoma limi strain BUZ 3(T), a Gram-negative bacterium, was isolated from coastal mud from the North Sea (Fedderwardersiel, Germany) and characterized using a polyphasic approach in 2011. The genome consists of a chromosome of about 7.5 Mb and three plasmids.
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29
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Genome sequence of Fibrella aestuarina BUZ 2(T), a filamentous marine bacterium. J Bacteriol 2012; 194:3555. [PMID: 22689241 DOI: 10.1128/jb.00550-12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fibrella aestuarina BUZ 2(T) is the type strain of the recently characterized genus Fibrella. Here we report the draft genome sequence of this strain, which consists of a single scaffold representing the chromosome (with 11 gaps) and a 161-kb circular plasmid.
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30
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Copeland A, Zhang X, Misra M, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Djao ODN, Göker M, Sikorski J, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Stand Genomic Sci 2012; 6:145-54. [PMID: 22768358 PMCID: PMC3387789 DOI: 10.4056/sigs.2475579] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Runella slithyformis Larkin and Williams 1978 is the type species of the genus Runella, which belongs to the Cytophagaceae, a family that was only recently classified to the order Cytophagales in the class Cytophagia. The species is of interest because it is able to grow at temperatures as low as 4°C. This is the first completed genome sequence of a member of the genus Runella and the sixth sequence from the family Cytophagaceae. The 6,919,729 bp long genome consists of a 6.6 Mbp circular genome and five circular plasmids of 38.8 to 107.0 kbp length, harboring a total of 5,974 protein-coding and 51 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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31
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Meyer TE, Kyndt JA, Memmi S, Moser T, Colón-Acevedo B, Devreese B, Van Beeumen JJ. The growing family of photoactive yellow proteins and their presumed functional roles. Photochem Photobiol Sci 2012; 11:1495-514. [DOI: 10.1039/c2pp25090j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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32
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Thomas F, Hehemann JH, Rebuffet E, Czjzek M, Michel G. Environmental and gut bacteroidetes: the food connection. Front Microbiol 2011; 2:93. [PMID: 21747801 PMCID: PMC3129010 DOI: 10.3389/fmicb.2011.00093] [Citation(s) in RCA: 667] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 04/14/2011] [Indexed: 12/21/2022] Open
Abstract
Members of the diverse bacterial phylum Bacteroidetes have colonized virtually all types of habitats on Earth. They are among the major members of the microbiota of animals, especially in the gastrointestinal tract, can act as pathogens and are frequently found in soils, oceans and freshwater. In these contrasting ecological niches, Bacteroidetes are increasingly regarded as specialists for the degradation of high molecular weight organic matter, i.e., proteins and carbohydrates. This review presents the current knowledge on the role and mechanisms of polysaccharide degradation by Bacteroidetes in their respective habitats. The recent sequencing of Bacteroidetes genomes confirms the presence of numerous carbohydrate-active enzymes covering a large spectrum of substrates from plant, algal, and animal origin. Comparative genomics reveal specific Polysaccharide Utilization Loci shared between distantly related members of the phylum, either in environmental or gut-associated species. Moreover, Bacteroidetes genomes appear to be highly plastic and frequently reorganized through genetic rearrangements, gene duplications and lateral gene transfers (LGT), a feature that could have driven their adaptation to distinct ecological niches. Evidence is accumulating that the nature of the diet shapes the composition of the intestinal microbiota. We address the potential links between gut and environmental bacteria through food consumption. LGT can provide gut bacteria with original sets of utensils to degrade otherwise refractory substrates found in the diet. A more complete understanding of the genetic gateways between food-associated environmental species and intestinal microbial communities sheds new light on the origin and evolution of Bacteroidetes as animals’ symbionts. It also raises the question as to how the consumption of increasingly hygienic and processed food deprives our microbiota from useful environmental genes and possibly affects our health.
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Affiliation(s)
- François Thomas
- UMR 7139, Marine Plants and Biomolecules, Station Biologique de Roscoff, UPMC University Paris 6, Roscoff, France
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Abt B, Teshima H, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Leadbetterella byssophila type strain (4M15). Stand Genomic Sci 2011; 4:2-12. [PMID: 21475582 PMCID: PMC3072089 DOI: 10.4056/sigs.1413518] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Leadbetterella byssophila Weon et al. 2005 is the type species of the genus Leadbetterella of the family Cytophagaceae in the phylum Bacteroidetes. Members of the phylum Bacteroidetes are widely distributed in nature, especially in aquatic environments. They are of special interest for their ability to degrade complex biopolymers. L. byssophila occupies a rather isolated position in the tree of life and is characterized by its ability to hydrolyze starch and gelatine, but not agar, cellulose or chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. L. byssophila is already the 16th member of the family Cytophagaceae whose genome has been sequenced. The 4,059,653 bp long single replicon genome with its 3,613 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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