Cho, Sang-Hyeok
(Department of Biological Sciences, Korea Advanced Institute of Science and Technology)
,
Jeong, Yujin
(Department of Biological Sciences, Korea Advanced Institute of Science and Technology)
,
Lee, Eunju
(Department of Biological Sciences, Korea Advanced Institute of Science and Technology)
,
Ko, So-Ra
(Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology)
,
Ahn, Chi-Yong
(Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology)
,
Oh, Hee-Mock
(Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology)
,
Cho, Byung-Kwan
(Department of Biological Sciences, Korea Advanced Institute of Science and Technology)
,
Cho, Suhyung
(Department of Biological Sciences, Korea Advanced Institute of Science and Technology)
Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict t...
Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pan-genome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.
Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pan-genome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.
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가설 설정
Secondary metabolites production of Erythrobacter species. A. Secondary metabolite biosynthetic gene clusters were predicted in 17 Erythrobacter species. Color indicates the presence of the biosynthetic gene cluster.
Carotenoid biosynthesis of Erythrobacter species. A. The carotenoid biosynthetic pathway is presented. The astaxanthin, spirilloxanthin, and spheroidene pathways are highlighted.
KEGG Orthology categorized 1731 genes. B. Clusters of Orthologous Groups categorized 2481 genes.
The astaxanthin, spirilloxanthin, and spheroidene pathways are highlighted. B. Photosynthetic gene clusters are presented in 6 Erythrobacter species. C.
Photosynthetic gene clusters are presented in 6 Erythrobacter species. C. Average nucleotide identity-based phylogeny tree of the 17 Erythrobacter species. Aerobic anoxygenic photosynthetic bacteria are highlighted with asterisks and indicated in magenta.
제안 방법
They were then dried at a critical point in CO2. Finally, the samples were sputtered with gold in a sputter coater (SC502, Polaron) and observed using a scanning electron microscope and FEI Quanta 250 FEG (FEI, USA).
대상 데이터
Erythrobacter sp. 3-20A1M was isolated from the southern sea of GeoJe, South Korea (34°46′ N, 128°46′ E), in August 2016 and deposited in the Korea Collection for Type Cultures (KCTC; Accession #, KCTC 18715P). The specimen was cultured in marine broth 2216 (BD Difco, USA) or marine agar at 25℃.
3-20A1M, was assembled. Subsequent genotypic and pan-genome analyses were conducted to identify the bacterium.
이론/모형
0) [23]. The assembled genome sequence was assessed using BUSCO [24].
16s rRNA based phylogeny analysis was conducted using MEGA-X [16]. The evolutionary history was inferred using the Neighbor-Joining method and the evolutionary distances were computed using the p-distance method.
성능/효과
xanthus was predicted to contain 13 BGCs. However, an error may have caused excessive predictions due to the relatively large number of contigs in the draft genome compared to that of other species, and the PGAP result also showed a large number of unique genes in E. xanthus. To assess the presence of erroneous genome sequences, the genome assembly quality was confirmed using BUSCO, returning a ratio of duplication of 0.
7%. It was determined that the overall large number of genes or abundance of BGCs were not caused by duplication errors in the genome assembly process. While Erythrobacter sp.
At least two species maintained 4750 that were classified as dispensable genes. The number of unique genes in a species varied from 217 to 1312, with E. xanthus having the largest genome size and the largest number of unique genes.
Of the 2946 annotated CDSs, 2830 functional CDSs were identified, excluding 116 pseudogenes. The remaining 52 features were RNA genes, including genes of three complete rRNAs (5S, 16S, and 23S), 45 tRNAs, and four non-coding RNAs.
3-20A1M (TableS1). Their genome sizes varied between a minimum of 2.6 Mbp in E. nanhaisediminis to a maximum of 4.4 Mbp in E. xanthus (Fig. 3A), while their GC content ranged from 57.4% to 67.2%.
The difference in photosynthetic ability among Erythrobacter species depends on the presence of the PGC. Through the analysis of the KO ID annotations, six Erythrobacter species, E. litoralis, E. longus, E. lutimaris, E. marinus, E. odishensis, and E. zhengii, were found to have both PGC and spheroidene/sprilloxanthin pathways required for the production of photosynthetic pigments (Fig.5B and Table S5). The discovered PGC includes puf, encoding light-harvesting complex subunits; bch, for bacteriochlorophyll production; chl, for chlorophyll production; and crt, for additional carotenoid biosynthesis.
xanthus. To assess the presence of erroneous genome sequences, the genome assembly quality was confirmed using BUSCO, returning a ratio of duplication of 0.7%. It was determined that the overall large number of genes or abundance of BGCs were not caused by duplication errors in the genome assembly process.
참고문헌 (35)
1 Worden AZ Follows MJ Giovannoni SJ Wilken S Zimmerman AE Keeling PJ 2015 Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes Science 347 1257594 10.1126/science.1257594 25678667
4 Kolber ZS Gerald F Lang AS Beatty JT Blankenship RE VanDover CL 2001 Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean Science 292 2492 2495 10.1126/science.1059707 11431568
5 Zheng Q Lin W Liu Y Chen C Jiao N 2016 A comparison of 14 Erythrobacter genomes provides insights into the genomic divergence and scattered distribution of phototrophs Front. Microbiol. 7 984 10.3389/fmicb.2016.00984 27446024
6 SHIBA T SIMIDU U 1982 Erythrobacter longus gen. nov., sp. nov., an aerobic bacterium which contains bacteriochlorophyll a Int. J. Syst. Evol. Microbiol. 32 211 217 10.1099/00207713-32-2-211
7 Takaichi S 2009 Distribution and biosynthesis of carotenoids The Purple Phototrophic Bacteria Ed. Springer New York, USA 97 117 10.1007/978-1-4020-8815-5_6
8 Takaichi S Shimada K Ishidsu J-i 1990 Carotenoids from the aerobic photosynthetic bacterium, Erythrobacter longus : β-carotene and its hydroxyl derivatives Arch. Microbiol. 153 118 122 10.1007/BF00247807
9 Galasso C Corinaldesi C Sansone C 2017 Carotenoids from marine organisms: Biological functions and industrial applications Antioxidants 6 96 10.3390/antiox6040096 29168774
11 Breed MF Harrison PA Blyth C Byrne M Gaget V Gellie NJ 2019 The potential of genomics for restoring ecosystems and biodiversity Nat. Rev. Genet. 20 615 628 10.1038/s41576-019-0152-0 31300751
12 Cho S-H Lee E Ko S-R Jin S Song Y Ahn C-Y 2020 Elucidation of the biosynthetic pathway of Vitamin B groups and potential secondary metabolite gene clusters via genome analysis of a marine bacterium Pseudoruegeria sp. M32A2M J. Microbiol. Biotechnol. 30 505 514 10.4014/jmb.1911.11006 31986560
13 Roosaare M Puustusmaa M Möls M Vaher M Remm M 2018 PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads PeerJ. 6 e4588 10.7717/peerj.4588 29629246
14 Na S-I Kim YO Yoon S-H Baek I Chun J Ha S-m 2018 UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction J. Microbiol. 56 280 285 10.1007/s12275-018-8014-6 29492869
15 Stamatakis A 2014 RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Bioinformatics 30 1312 1313 10.1093/bioinformatics/btu033 24451623
16 Kumar S Stecher G Li M Knyaz C Tamura K 2018 MEGA X: molecular evolutionary genetics analysis across computing platforms Mol. Biol. Evol. 35 1547 1549 10.1093/molbev/msy096 29722887
17 Tatusova T DiCuccio M Badretdin A Chetvernin V Nawrocki EP Zaslavsky L 2016 NCBI prokaryotic genome annotation pipeline Nucleic Acids Res. 44 6614 6624 10.1093/nar/gkw569 27342282
18 Kanehisa M Sato Y Kawashima M Furumichi M Tanabe M 2015 KEGG as a reference resource for gene and protein annotation Nucleic Acids Res. 44 D457 D462 10.1093/nar/gkv1070 26476454
19 Tatusov RL Galperin MY Natale DA Koonin EV 2000 The COG database: a tool for genome-scale analysis of protein functions and evolution Nucleic Acids Res. 28 33 36 10.1093/nar/28.1.33 10592175
21 Muller J Szklarczyk D Julien P Letunic I Roth A Kuhn M 2010 eggNOG v2. 0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations Nucleic Acids Res 38 D190 D195 10.1093/nar/gkp951 19900971
23 Blin K Shaw S Steinke K Villebro R Ziemert N Lee SY 2019 antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline Nucleic Acids Res 47 W81 W87 10.1093/nar/gkz310 31032519
24 Simão FA Waterhouse RM Ioannidis P Kriventseva EV Zdobnov EM 2015 BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Bioinformatics 31 3210 3212 10.1093/bioinformatics/btv351 26059717
25 Li X Koblížek M Feng F Li Y Jian J Zeng Y 2013 Whole-genome sequence of a freshwater aerobic anoxygenic phototroph, Porphyrobacter sp. strain AAP82, isolated from the Huguangyan Maar Lake in Southern China Genome Announc. 1 e0007213 10.1128/genomeA.00072-13 23516203
26 Xu X-W Wu Y-H Wang C-S Wang X-G Oren A Wu M 2009 Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae Int. J. Syst. Evol. Microbiol. 59 2247 2253 10.1099/ijs.0.004267-0 19620383
27 Medini D Donati C Tettelin H Masignani V Rappuoli R 2005 The microbial pan-genome Curr. Opin. Genet. Dev. 15 589 594 10.1016/j.gde.2005.09.006 16185861
28 Dertli E Mayer MJ Colquhoun IJ Narbad A 2016 EpsA is an essential gene in exopolysaccharide production in Lactobacillus johnsonii FI9785 Microb. Biotechnol. 9 496 501 10.1111/1751-7915.12314 26401596
29 Domozych DS Sørensen I Popper ZA Ochs J Andreas A Fangel JU 2014 Pectin metabolism and assembly in the cell wall of the charophyte green alga Penium margaritaceum Plant Physiol. 165 105 118 10.1104/pp.114.236257 24652345
30 Coleman RJ Patel YN Harding NE 2008 Identification and organization of genes for diutan polysaccharide synthesis from Sphingomonas sp. ATCC 53159 J. Ind. Microbiol. Biotechnol. 35 263 274 10.1007/s10295-008-0303-3 18210176
31 Alvarez-Martinez CE Christie PJ 2009 Biological diversity of prokaryotic type IV secretion systems Microbiol. Mol. Biol. Rev. 73 775 808 10.1128/MMBR.00023-09 19946141
32 Minamino T 2018 Hierarchical protein export mechanism of the bacterial flagellar type III protein export apparatus FEMS Microbiol. Lett. 365 fny117 10.1093/femsle/fny117 29850796
34 Moskvin OV Gomelsky L Gomelsky M 2005 Transcriptome analysis of the Rhodobacter sphaeroides PpsR regulon: PpsR as a master regulator of photosystem development J. Bacteriol. 187 2148 2156 10.1128/JB.187.6.2148-2156.2005 15743963
35 Lee I Kim YO Park S-C Chun J 2016 OrthoANI: an improved algorithm and software for calculating average nucleotide identity Int. J. Syst. Evol. Microbiol. 66 1100 1103 10.1099/ijsem.0.000760 26585518
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