Title Page
Contents
CHAPTER 1. POLYPHASIC TAXONOMY OF NOVEL RADIATION-RESISTANT BACTERIA AND ANTI-INFLAMMATION EFFECTS 18
1. INTRODUCTION 18
1.1. Radiation-resistant bacteria 18
1.2. Polyphasic taxonomy in bacteria 20
1.3. Report of the genera of bacteria in this research 21
1.3.1. The genus Rhodocytophaga 21
1.3.2. The genus Nibribacter 21
1.3.3. The genus Larkinella 22
1.4. Inflammation 23
1.5. Deinococcus actinosclerus BM2 26
2. METHODS 28
2.1. Collected sample, condition and deposit of bacteria 28
2.2. Genotypic taxonomy in bacteria 30
2.2.1. 16S rRNA gene sequencing analysis 30
2.2.2. Phylogenetic analysis 31
2.2.3. Genome sequencing 32
2.3. Chemotaxonomy in bacteria 33
2.3.1. Fatty acid in bacteria[내용없음] 8
2.3.2. Polar lipid & isoprenoid quinone analysis 35
2.4. Phenotypic taxonomy in bacteria 36
2.5. Radiation-resistance analysis in bacteria 37
2.5.1. Gamma & ultraviolet radiation-resistance analysis 37
2.6. Anti-inflammation & antioxidant effects analysis 40
2.6.1. Chemicals and reagents 40
2.6.2. BM2U extract preparation 41
2.6.3. DPPH radical scavenging activity 43
2.6.4. Cell culture 44
2.6.5. MTT assay 44
2.6.6. Quantitative real-time polymerase chain reaction (qRT-PCR) 45
2.6.7. Immunoblot analysis 47
2.6.8. Statistical analysis 48
3. RESULTS 49
3.1. Rhodocytophaga rosea sp. nov. strain 172606-1 49
3.1.1. Phylogenetic analysis 49
3.1.2. Morphological, physiological, and biochemical characterization 51
3.1.3. Chemotaxonomic characterization 55
3.1.4. Genome sequencing 58
3.2. Nibribacter ruber sp. nov. strain BT10 60
3.2.1. Phylogenetic analysis 60
3.2.2. Morphological, physiological, and biochemical characterization 62
3.2.3. Chemotaxonomic characterization 66
3.2.4. Genome sequencing 69
3.3. Larkinella humicola sp. nov. strain MA1 71
3.3.1. Phylogenetic analysis 71
3.3.2. Morphological, physiological, and biochemical characterization 73
3.3.3. Chemotaxonomic characterization 76
3.3.4. Genome sequencing 79
3.4. Radiation survival test 81
3.4.1. Gamma radiation survival test 81
3.4.2. UV radiation survival test 83
3.4.3. Genome of radiation resistance 85
3.5. Taxonomic conclusion 87
3.5.1. Rhodocytophaga rosea sp. nov. (strain 172606-1T)[이미지참조] 87
3.5.2. Nibribacter ruber sp. nov. (strain BT10T)[이미지참조] 87
3.4.3. Larkinella humicola sp. nov. (strain MA1T)[이미지참조] 88
3.6. Anti-inflammation effects of Deinococcus actinosclerus BM2 89
3.6.1. Antioxidant Capacities of BM2U 89
3.6.2. Cell cytotoxicity 91
3.6.3. Suppressive effect of BM2U on LPS-mediated TNF-α, IL-1β, and IL-6 expression 93
3.6.4. Suppressive effect of BM2U on COX-2 and iNOS expression 95
3.6.5. Effect of BM2U on LPS-Mediated Activation of MAPKs 97
3.6.6. Effect of BM2U on HO-1 Expression 99
4. DISCUSSION 101
4.1. Description of Rhodocytophaga rosea sp. nov 101
4.2. Description of Nibribacter ruber sp. nov. 102
4.3. Description of Larkinella humicola sp. nov. 103
4.4. Discussion 104
4.4.1. Isolation of novel radiation-resistant bacteria 104
4.4.2. Anti-inflammation effects on radiation-resistant bacteria 105
CHAPTER 2. TAXONOMY OF NOVEL YEASTS 109
1. INTRODUCTION 109
1.1. Yeasts 109
1.2. Basidiomycetous Yeasts 112
1.3. Report of the genus Vishniacozyma 113
2. METHODS 114
2.1. Collected Sample, Condition and Deposit of Yeast 114
2.2. Genotypic Taxonomy 117
2.2.1. D1/D2 and ITS rRNA gene sequencing analysis 117
2.2.2. Phylogenetic analysis 118
2.3. Phenotypic Taxonomy 119
3. RESULTS 121
3.1. Genotypic Taxonomy 121
3.2. Phenotypic Taxonomy 124
3.3. Taxonomic conclusion 127
4. DESCRIPTION OF NOVEL SPECIES 128
REFERENCE 130
ABSTRACT 145
국문요약 150
Table 1. Information of isolated strains and type strains 29
Table 2. The primer sequence for qRT-PCR 46
Table 3. Different characteristics of Rhodocytophaga rosea 172606-1T sp. nov., and closely related species.[이미지참조] 54
Table 4. Cellular fatty acid profiles of Rhodocytophaga rosea 172606-1T sp. nov., and closely related species.[이미지참조] 56
Table 5. Different characteristics of Nibribacter ruber BT10T sp. nov., and closely related species.[이미지참조] 65
Table 6. Cellular fatty acid profiles of Nibribacter ruber BT10T sp. nov., and closely related species.[이미지참조] 67
Table 7. Different characteristics of Larkinella humicola MA1T sp. nov., and closely related species.[이미지참조] 75
Table 8. Cellular fatty acid profiles of Larkinella humicola MA1T sp. nov., and closely related species.[이미지참조] 77
Table 9. Presence of DNA repair genes involved in the excision repair pathways compared with Deinococcus radiodurans NBRC 15346T.[이미지참조] 86
Table 10. Information of isolated strains and type strains 115
Table 11. List of strains, localities, substrates of isolation of collection and DNA sequences used in this study 116
Table 12. Number of nucleotide substitutions in the D1/D2 domain and ITS region sequences among the strains and closely related species. The upper right triangle shows the number of nucleotide differences and the gaps (in parentheses)... 122
Table 13. Phenotypic characteristics that differentiate V. terrae sp. nov. and related species, V. peneaus and V. phoenicis. 126
Figure 1. Phylogenetic distribution of radiation-resistant organisms. Trefoils indicate radiation resistant members. 19
Figure 2. M1 and M2 polarization of macrophages 25
Figure 3. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of BM2T[이미지참조] 27
Figure 4. Preparation of fatty acids sample 34
Figure 5. The bacteria was irradiated by a cobalt-60-based gamma irradiator. 38
Figure 6. Ultraviolet crosslinker (UVP, CX-2000, CA, USA) 39
Figure 7. Extraction method of the BM2U 42
Figure 8. A neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 16S rRNA gene sequences showing the... 50
Figure 9. Transmission electron micrograph image of strain 172606-1T. Cell morphology was determined by a TEM after growth on R2A for...[이미지참조] 53
Figure 10. Two-dimensional chromatography of polar lipids of strain 172606-1T.[이미지참조] 57
Figure 11. Genome-based phylogenetic tree showing the phylogenetic relationship of strain 172606-1T with the closely related species. The...[이미지참조] 59
Figure 12. A neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 16S rRNA gene sequences showing the... 61
Figure 13. Transmission electron micrograph image of strain BT10T. Cell morphology was determined by a TEM after growth on R2A for...[이미지참조] 64
Figure 14. Two-dimensional chromatography of polar lipids of strain BT10T. The TLC plates were detected with molybdatophosphoric acid,...[이미지참조] 68
Figure 15. Genome-based phylogenetic tree showing the phylogenetic relationship of strain BT10T with the closely related species. The...[이미지참조] 70
Figure 16. A neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 16S rRNA gene sequences showing the... 72
Figure 17. Transmission electron micrograph image of strain MA1T. Cell morphology was determined by a TEM after growth on R2A for 3...[이미지참조] 74
Figure 18. Two-dimensional chromatography of polar lipids of strain MA1T. The TLC plates were detected with molybdatophosphoric acid,...[이미지참조] 78
Figure 19. Genome-based phylogenetic tree showing the phylogenetic relationship of strain BT10T with the closely related species. The...[이미지참조] 80
Figure 20. Survival plots for the D. radiodurans DSM 20539T (▲), strain MA1T (●), strain 172606-1T (■), strain BT10T (△), and E. coli...[이미지참조] 82
Figure 21. Survival plots for the D. radiodurans DSM 20539T (▲), strain MA1T (●), strain 172606-1T (■), strain BT10T (△), and E. coli...[이미지참조] 84
Figure 22. Effect of BM2U on DPPH radical scavenging activity. The antioxidant capacities of BM2U were determined through the DPPH... 90
Figure 23. Cell cytotoxicity of BM2U on RAW264.7. RAW264.7 macrophages were incubated with different doses of BM2U for 24 h,... 92
Figure 24. Effect of BM2U on LPS-mediated TNF-α, IL-1β, and IL-6 mRNA expression. RAW264.7 macrophage cells were challenged with... 94
Figure 25. Effect of BM2U on LPS-mediated COX-2 and iNOS expression. RAW264.7 macrophage cells were challenged with LPS (1... 96
Figure 26. Effect of BM2U on LPS-mediated JNK, ERK, and p38 MAPK activation. RAW264.7 macrophage cells were challenged with... 98
Figure 27. Effect of BM2U on the induction of HO-1. RAW264.7 macrophages were treated with BM2U (0.2-20 μg/ml) for 24 h. HO-1... 100
Figure 28. Various disciplines in yeast biotechnology. 110
Figure 29. Various forms of yeast budding. (A) Polar budding; (B) Mono-polar budding; (C) Bipolar budding; (D) Multilateral budding. 111
Figure 30. Phylogenetic tree based on the concatenated sequences of the D1/D2 region of the LSU rRNA gene and ITS regions and... 123
Figure 31. Budding cells of V. terrae sp. nov. The polar budding cells of V. terrae YP344T on YM agar after three days at 10 ℃.[이미지참조] 125