Abstract
Here, we present the draft genome sequence of a novel carotenoid 2′-isopentenylsaproxanthin producer, Jejuia pallidilutea strain 11shimoA1, isolated from the surface of seaweed in Japan, and the ethyl methanesulfonate-induced pigmentation mutants. This genomic information will help to not only elucidate the 2′-isopentenylsaproxanthin biosynthetic pathway but also understand the evolution of flavobacteria.
GENOME ANNOUNCEMENT
The family Flavobacteriaceae was established for grouping a diverse array of bacteria showing Gram-negative, aerobic, nonmotile pigmented bacteria that show yellow to orange colored colonies (1) and includes more than 114 genera (http://www.bacterio.net). One of the genera, Jejuia, was proposed in 2009 for nonmotile, yellow, nondiffusible pigment producers in seawater and consists of a single species J. pallidilutea (2, 3). More recently, Takatani et al. (4) have identified a strain 11shimoA1 isolated from the surface of seaweed that produces not only zeaxanthin but also a new monocyclic carotenoid, 2′-isopentenylsaproxanthin. The amount of 2′-isopentenylsaproxanthin production increased under alkaline conditions (4). However, carotenoid synthetic pathways of the 2′-isopentenylsaproxanthin have not been resolved yet.
The genome sequences of J. pallidilutea 11shimoA1 (JCM 19538) and the pigmentation mutants induced by ethyl methanesulfonate were sequenced with the Illumina HiSeq (Illumina) and Ion PGM systems (Life Technologies, Carlsbad, CA), respectively. The genome sequence of 11shimoA1 was de novo assembled using Velvet version 1.2.08. Those mutants were de novo assembled using Newbler version 2.8. The annotation and genome analysis were performed by RAST (Rapid Annotation Subsystem Technology) (5). The sizes of the draft genome of J. pallidilutea 11shimoA1, the pigment-deficient mutant A1W, and the red-pigmented mutant A1R were 3,805,351 bp, 3,773,436 bp, and 3,770,805 bp, comprising 98, 75, and 87 contigs with G+C contents of 33.9%, 33.9%, and 33.8%, respectively. These redundancies were 779, 20, and 17, and N50 contig lengths were 244,792 bp, 135,822 bp, and 112,803 bp, respectively. Putative coding sequences (CDS) were 3,328, 4,046, and 4,232; rRNA sequences were 3, 3, and 3; tRNA sequences were 36, 34, and 35 for strains 11shimoA1, A1W, and A1R, respectively. The strain 11shimoA1 possessed a set of carotenoid biosynthesis gene clusters (phytoene dehydrogenase, phytoene synthase, β-carotene hydroxylase and lycopene β cyclase), but the other set of phytoene dehydrogenase and lycopene elongase was located on a different locus of the genome. It is suggested that these genes may be responsible for producing zeaxanthin and 2′-isopentenylsaproxanthin. In addition, genome comparisons between the genomes of 11shimoA1 and A1W revealed a frameshift in the phytoene dehydrogenase gene of the A1W genome. These strains have been deposited in the Japan Collection of Microorganisms as JCM 19301 (A1W) and JCM 19302 (A1R), respectively.
Nucleotide sequence accession numbers.
The genome data have been deposited in DDBJ/EMBL/GenBank under the accession numbers BBNY01000001 to BBNY01000098, BBNR01000001 to BBNR01000075, and BBNS01000001 to BBNS01000087 for Jejuia pallidilutea strains 11shimoA1, A1W, and A1R, respectively.
ACKNOWLEDGMENTS
This work was supported by the Genome Information Upgrading Program of the National BioResource Project from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan (to M. Hattori and M. Ohkuma), the Strategic Japanese-Brazilian Cooperative Program, Biomass & Bioenergy (to Tomoo Sawabe), and Kaken (26660168) (to Tomoo Sawabe). P. Meirelles thanks CAPES for the Ph.D. scholarship (4848-14-9 CAPES/JSPS).
Footnotes
Citation Takatani N, Nakanishi M, Meirelles P, Mino S, Suda W, Oshima K, Hattori M, Ohkuma M, Hosokawa M, Miyashita K, Thompson FL, Niwa A, Sawabe T, Sawabe T. 2014. Draft genome sequence of marine flavobacterium Jejuia pallidilutea strain 11shimoA1 and pigmentation mutants. Genome Announc. 2(6):e01236-14. doi: 10.1128/genomeA.01236-14.
REFERENCES
- 1. Holmes B, Owen RJ, McMeekin TA. 1984. Genus I: Flavobacterium Bergey, Harrison, Breed, Hammer and Huntoon. 1923, 97AL emend. Bernardet, Segers, Vancanneyt, Berthe, Kersters and Vandamme 1996, 139. p 353–361 In Krieg NR, Holt JG. (ed), Bergey’s manual of systematic bacteriology, vol. 1 Williams & Wilkins, Baltimore. [Google Scholar]
- 2. Lee DH, Kahng HY, Lee YS, Jung JS, Kim JM, Chung BS, Park SK, Jeon CO. 2009. Jejuia pallidilutea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from seawater. Int. J. Syst. Evol. Microbiol. 59:2148–2152. 10.1099/ijs.0.007625-0. [DOI] [PubMed] [Google Scholar]
- 3. Park SC, Choe HN, Hwang YM, Baik KS, Kim SN, Lee YS, Jung JS, Seong CN. 2013. Marinivirga aestuarii gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from marine environments, and emended descriptions of the genera Hyunsoonleella, Jejuia and Pontirhabdus and the species Hyunsoonleella jejuensis, Jejuia pallidilutea and Pontirhabdus pectinivorans. Int. J. Syst. Evol. Microbiol. 63:1524–1531. 10.1099/ijs.0.042341-0. [DOI] [PubMed] [Google Scholar]
- 4. Takatani N, Nishida K, Sawabe T, Maoka T, Miyashita K, Hosokawa M. 2014. Identification of a novel carotenoid, 2′-isopentenylsaproxanthin, by Jejuia pallidilutea strain 11shimoA1 and its increased production under alkaline condition. Appl. Microbiol. Biotechnol. 98:6633–6640. 10.1007/s00253-014-5702-y. [DOI] [PubMed] [Google Scholar]
- 5. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75–89. 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]