Genome Sequence of Citromicrobium Strain JLT1363, Isolated from the South China Sea

Zheng, Qiang; Zhang, Rui; Jiao, Nianzhi

doi:10.1128/jb.00121-11

Cited by 10 publications

(4 citation statements)

References 14 publications

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“…The same amino acids at these positions were also found in rhodopsins of the strains 4H-3-7-5, Gillisia limnaea R-8282 T ( = DSM 15749) [51], [52], Truepera radiovictrix RQ-24 T ( = DSM 17093) [53], [54], Citromicrobium bathyomarinum JL354 [55], Citromicrobium sp. JLT1363 [56], Fulvimarina pelagi HTCC2106 T [57] and Phycisphaera mikurensis NBRC 102666 T . At position 105, which is mainly responsible for rhodopsin spectral tuning, the amino acid residue Leu (L) was detected [50].…”

Section: Resultsmentioning

confidence: 99%

Genomics and Physiology of a Marine Flavobacterium Encoding a Proteorhodopsin and a Xanthorhodopsin-Like Protein

et al. 2013

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Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. Expression analyses by RT-PCR and direct mRNA-sequencing showed that both rhodopsins and the complete β-carotene pathway necessary for retinal production are transcribed in PRO95. Proton translocation measurements showed enhanced proton pump activity in response to light, supporting that one or both rhodopsins are functional. Genomic information and carbon source respiration data were used to develop a defined cultivation medium for PRO95, but reproducible growth always required small amounts of yeast extract. Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations. Starvation or stress conditions might be needed to observe the physiological effect of light induced energy acquisition.

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Section: Resultsmentioning

confidence: 99%

Genomics and Physiology of a Marine Flavobacterium Encoding a Proteorhodopsin and a Xanthorhodopsin-Like Protein

et al. 2013

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“…The genomes of two marine bacteria, namely, the oligotroph Citromicrobium bathyomarinum JL354 [31] and Citromicrobium sp. JLT1363 [32] from the order Sphingomonadales , were sequenced and annotated, and TBDTs were found to be abundant in their genomes. Moreover, the protein expression profiles of cells show that TBDTs were involved in coping with the low levels of nutrients during the stationary phase.…”

Section: Introductionmentioning

confidence: 99%

Distribution and Functions of TonB-Dependent Transporters in Marine Bacteria and Environments: Implications for Dissolved Organic Matter Utilization

et al. 2012

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BackgroundBacteria play critical roles in marine nutrient cycles by incorporating and redistributing dissolved organic matter (DOM) and inorganic nutrients in the ocean. TonB-dependent transporter (TBDT) proteins allow Gram-negative bacteria to take up scarce resources from nutrient-limiting environments as well as siderophores, heme, vitamin B12, and recently identified carbohydrates. Thus, the characterization of TBDT distribution and functions is essential to better understand the contribution TBDT to DOM assimilation and its consequences on nutrient cycling in the environment.Methodology/Principal FindingsThis study presents the distribution of encoded known and putative TBDT proteins in the genomes of microorganisms and from the Global Ocean Survey data. Using a Lek clustering algorithm and substrate specificities, the TBDT sequences were mainly classified into the following three groups: (1) DOM transporters; (2) Siderophores/Vitamins transporters; and (3) Heme/Hemophores/Iron(heme)-binding protein transporters. Diverse TBDTs were found in the genomes of oligotroph Citromicrobium bathyomarinum JL354 and Citromicrobium sp JLT1363 and were highly expressed in the stationary phase of bacterial growth. The results show that the Gammaproteobacteria and the Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria accounted for the majority of the TBDT gene pool in marine surface waters.Conclusions/SignificanceThe results of this study confirm the ecological importance of TBDTs in DOM assimilation for bacteria in marine environments owing to a wide range of substrate utilization potential in the ubiquitous Gammaproteobacteria and CFB group bacteria.

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“…; Zheng et al. ); Fulvimarina pelagi HTCC2506 T from the western Sargasso Sea (Kang et al. ); Parvularcula oceanus JLT2013 T from deep‐sea water of the southeastern Pacific Ocean (Li et al.…”

Section: Resultsmentioning

confidence: 99%

Diversity and functional analysis of light‐driven pumping rhodopsins in marine Flavobacteria

et al. 2015

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The aims of this study are the description of diversity for proteorhodopsin (PR)‐containing flavobacteria in marine environments, the finding of novel photoreceptive membrane proteins, and the elucidation of the effect of light on the growth of three rhodopsin genes containing flavobacterium. We investigated novel sodium ion rhodopsin (NaR) and halorhodopsin (HR) genes from PR‐containing flavobacteria that were previously isolated from diverse aquatic sites, mainly from tidal flat sediment (62.5%). In 16 PR‐containing isolates, three new types of genes were found. Among these three isolates, one (Nonlabens sp. YIK11 isolated from sediment) contained both the NaR and chloride ion rhodopsin (ClR) ‐ HR type of gene. The sequences showed that the DTE (proton pump), NDQ (sodium ion pump) and NTQ (chloride ion pump) motifs corresponding to the D85, T89, and D96 positions in bacteriorhodopsin (BR) were well conserved. Phylogenetic analysis indicated that three NaR and one ClR grouped within the same clade, as previously reported. Illumination of cell suspensions showed the change in proton pump activity, supporting that one or more rhodopsins are functional. The qRT‐PCR study revealed that three rhodopsin genes, especially NaR, are highly induced when they are incubated in the presence of light or in the absence of sufficient nutrients. The expression levels of the DTE, NDQ, and NTQ motif‐containing rhodopsin genes in YIK11 correlate positively with illumination, but negatively with nutrient levels. Based on those results, we concluded that light has a positive impact on the relative expression levels of the three rhodopsin genes in the flavobacterium, Nonlabens sp. YIK11, but with no apparent positive impact on growth. Consequently, light did not stimulate the growth of YIK11 as determined by cell numbers in a nutrient‐limited or ‐enriched medium, although it contains and induces three rhodopsins.

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Genome Sequence of Citromicrobium Strain JLT1363, Isolated from the South China Sea

Cited by 10 publications

References 14 publications

Genomics and Physiology of a Marine Flavobacterium Encoding a Proteorhodopsin and a Xanthorhodopsin-Like Protein

Genomics and Physiology of a Marine Flavobacterium Encoding a Proteorhodopsin and a Xanthorhodopsin-Like Protein

Distribution and Functions of TonB-Dependent Transporters in Marine Bacteria and Environments: Implications for Dissolved Organic Matter Utilization

Diversity and functional analysis of light‐driven pumping rhodopsins in marine Flavobacteria

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