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  • 1
    Online Resource
    Online Resource
    Characterization of a cryptic plasmid pSM429 and its application for heterologous expression in psychrophilic Pseudoalteromonas
    Springer Science and Business Media LLC ; 2011
    In:  Microbial Cell Factories Vol. 10, No. 1 ( 2011-12)
    Details
    In: Microbial Cell Factories, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2011-12)
    Abstract: Pseudoalteromonas is an important genus widespread in marine environment, and a lot of psychrophilic Pseudoalteromonas strains thrive in deep sea and polar sea. By now, there are only a few genetic systems for Pseudoalteromonas reported and no commercial Pseudoalteromonas genetic system is available, which impedes the study of Pseudoalteromonas , especially for psychrophilic strains. The aim of this study is to develop a heterologous expression system for psychrophilic Pseudoalteromonas . Results A cryptic plasmid pSM429 isolated from psychrophilic Pseudoalteromonas sp. BSi20429 from the Arctic sea ice, was sequenced and characterized. The plasmid pSM429 is 3874 bp in length, with a G+C content of 28%. Four putative open reading frames (ORFs) were identified on pSM429. Based on homology, the ORF4 was predicted to encode a replication initiation (Rep) protein. A shuttle vector ( Escherichia coli, Pseudoalteromonas ), pWD, was constructed by ligating pSM429 and pUC19 and inserting a chloramphenicol acetyl transferase (CAT) cassette conferring chloramphenicol resistance. To determine the minimal replicon of pSM429 and to check the functionality of identified ORFs, various pWD derivatives were constructed. All derivatives except the two smallest ones were shown to allow replication in Pseudoalteromonas sp. SM20429, a plasmid-cured strain of Pseudoalteromonas sp. BSi20429, suggesting that the orf4 and its flanking intergenic regions are essential for plasmid replication. Although not essential, the sequence including some repeats between orf1 and orf2 plays important roles in segregational stability of the plasmid. With the aid of pWD-derived plasmid pWD2, the erythromycin resistance gene and the cd gene encoding the catalytic domain of a cold-adapted cellulase were successfully expressed in Pseudoalteromonas sp. SM20429. Conclusions Plasmid pSM429 was isolated and characterized, and the regions essential for plasmid replication and stability were determined, helping the development of pSM429-based shuttle vectors. The shuttle vectors pWD and its derivatives could be used as cloning vectors for Pseudoalteromonas , offering new perspectives in the genetic manipulation of Pseudoalteromonas strains. With the aid of pWD-derived vector and its host, the erythromycin resistance gene and the cd gene of a cold-adapted protein were successfully expressed, indicating that the potential use of this system for recombinant protein production, especially for cold-adapted proteins.
    Type of Medium: Online Resource
    ISSN: 1475-2859
    URL: Article
    DOI: 10.1186/1475-2859-10-30
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2011
    detail.hit.zdb_id: 2091377-1
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  • 2
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    Distribution of bacterial genes driving dimethyl sulfide cycling in the polar oceans
    Springer Science and Business Media LLC ; 2021
    In:  Microbiome Vol. 9, No. 1 ( 2021-10-16)
    Details
    In: Microbiome, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2021-10-16)
    Abstract: Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bacteria and phytoplankton. Polar oceans, which represent about one fifth of Earth’s surface, contribute significantly to the global oceanic DMS sea-air flux. However, a global overview of DMS and DMSP cycling in polar oceans is still lacking and the key genes and the microbial assemblages involved in DMSP/DMS transformation remain to be fully unveiled. Results Here, we systematically investigated the biogeographic traits of 16 key microbial enzymes involved in DMS/DMSP cycling in 60 metagenomic samples from polar waters, together with 174 metagenome and 151 metatranscriptomes from non-polar Tara Ocean dataset. Our analyses suggest that intense DMS/DMSP cycling occurs in the polar oceans. DMSP demethylase (DmdA), DMSP lyases (DddD, DddP, and DddK), and trimethylamine monooxygenase (Tmm, which oxidizes DMS to dimethylsulfoxide) were the most prevalent bacterial genes involved in global DMS/DMSP cycling. Alphaproteobacteria (Pelagibacterales) and Gammaproteobacteria appear to play prominent roles in DMS/DMSP cycling in polar oceans. The phenomenon that multiple DMS/DMSP cycling genes co-occurred in the same bacterial genome was also observed in metagenome assembled genomes (MAGs) from polar oceans. The microbial assemblages from the polar oceans were significantly correlated with water depth rather than geographic distance, suggesting the differences of habitats between surface and deep waters rather than dispersal limitation are the key factors shaping microbial assemblages involved in DMS/DMSP cycling in polar oceans. Conclusions Overall, this study provides a global overview of the biogeographic traits of known bacterial genes involved in DMS/DMSP cycling from the Arctic and Antarctic oceans, laying a solid foundation for further studies of DMS/DMSP cycling in polar ocean microbiome at the enzymatic, metabolic, and processual levels.
    Type of Medium: Online Resource
    ISSN: 2049-2618
    URL: Article
    URL: Article
    DOI: 10.1186/s40168-021-01153-3
    DOI: 10.21203/rs.3.rs-1405853/v1
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2697425-3
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  • 3
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    Correction to: Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans
    Springer Science and Business Media LLC ; 2021
    In:  Microbiome Vol. 9, No. 1 ( 2021-12)
    Details
    In: Microbiome, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2021-12)
    Type of Medium: Online Resource
    ISSN: 2049-2618
    URL: Article
    DOI: 10.1186/s40168-021-01182-y
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2697425-3
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  • 4
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    Development of a genetic system for the deep-sea psychrophilic bacterium Pseudoalteromonas sp. SM9913
    Springer Science and Business Media LLC ; 2014
    In:  Microbial Cell Factories Vol. 13, No. 1 ( 2014-12)
    Details
    In: Microbial Cell Factories, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2014-12)
    Type of Medium: Online Resource
    ISSN: 1475-2859
    URL: Article
    DOI: 10.1186/1475-2859-13-13
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2014
    detail.hit.zdb_id: 2091377-1
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  • 5
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    d -Alanine Metabolism via d- Ala Aminotransferase by a Marine Gammaproteobacterium, Pseudoalteromonas sp. Strain CF6-2
    American Society for Microbiology ; 2022
    In:  Applied and Environmental Microbiology Vol. 88, No. 3 ( 2022-02-08)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 88, No. 3 ( 2022-02-08)
    Abstract: As the most abundant d- amino acid (DAA) in the ocean, d- alanine ( d -Ala) is a key component of peptidoglycan in the bacterial cell wall. However, the underlying mechanisms of bacterial metabolization of d- Ala through the microbial food web remain largely unknown. In this study, the metabolism of d- Ala by marine bacterium Pseudoalteromonas sp. strain CF6-2 was investigated. Based on genomic, transcriptional, and biochemical analyses combined with gene knockout, d- Ala aminotransferase was found to be indispensable for the catabolism of d- Ala in strain CF6-2. Investigation on other marine bacteria also showed that d- Ala aminotransferase gene is a reliable indicator for their ability to utilize d- Ala. Bioinformatic investigation revealed that d- Ala aminotransferase sequences are prevalent in genomes of marine bacteria and metagenomes, especially in seawater samples, and Gammaproteobacteria represents the predominant group containing d- Ala aminotransferase. Thus, Gammaproteobacteria is likely the dominant group to utilize d- Ala via d- Ala aminotransferase to drive the recycling and mineralization of d- Ala in the ocean. IMPORTANCE As the most abundant d- amino acid in the ocean, d- Ala is a component of the marine DON (dissolved organic nitrogen) pool. However, the underlying mechanism of bacterial metabolization of d- Ala to drive the recycling and mineralization of d- Ala in the ocean is still largely unknown. The results in this study showed that d- Ala aminotransferase is specific and indispensable for d- Ala catabolism in marine bacteria and that marine bacteria containing d- Ala aminotransferase genes are predominantly Gammaproteobacteria widely distributed in global oceans. This study reveals marine d- Ala-utilizing bacteria and the mechanism of their metabolization of d- Ala. The results shed light on the mechanisms of recycling and mineralization of d- Ala driven by bacteria in the ocean, which are helpful in understanding oceanic microbial-mediated nitrogen cycle.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/aem.02219-21
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 6
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    Diaminopimelic Acid Metabolism by Pseudomonadota in the Ocean
    American Society for Microbiology ; 2022
    In:  Microbiology Spectrum Vol. 10, No. 5 ( 2022-10-26)
    Details
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 10, No. 5 ( 2022-10-26)
    Abstract: Diaminopimelic acid (DAP) is a unique component of the cell wall of Gram-negative bacteria. It is also an important component of organic matter and is widely utilized by microbes in the world’s oceans. However, neither DAP concentrations nor marine DAP-utilizing microbes have been investigated. Here, DAP concentrations in seawater were measured and the diversity of marine DAP-utilizing bacteria and the mechanisms for their DAP metabolism were investigated. Free DAP concentrations in seawater, from surface to a 5,000 m depth, were found to be between 0.61 μM and 0.96 μM in the western Pacific Ocean. DAP-utilizing bacteria from 20 families in 4 phyla were recovered from the western Pacific seawater and 14 strains were further isolated, in which Pseudomonadota bacteria were dominant. Based on genomic and transcriptomic analyses combined with gene deletion and in vitro activity detection, DAP decarboxylase (LysA), which catalyzes the decarboxylation of DAP to form lysine, was found to be a key and specific enzyme involved in DAP metabolism in the isolated Pseudomonadota strains. Interrogation of the Tara Oceans database found that most LysA-like sequences (92%) are from Pseudomonadota , which are widely distributed in multiple habitats. This study provides an insight into DAP metabolism by marine bacteria in the ocean and contributes to our understanding of the mineralization and recycling of DAP by marine bacteria. IMPORTANCE DAP is a unique component of peptidoglycan in Gram-negative bacterial cell walls. Due to the large number of marine Gram-negative bacteria, DAP is an important component of marine organic matter. However, it remains unclear how DAP is metabolized by marine microbes. This study investigated marine DAP-utilizing bacteria by cultivation and bioinformational analysis and examined the mechanism of DAP metabolism used by marine bacteria. The results demonstrate that Pseudomonadota bacteria are likely to be an important DAP-utilizing group in the ocean and that DAP decarboxylase is a key enzyme involved in DAP metabolism. This study also sheds light on the mineralization and recycling of DAP driven by bacteria.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    URL: Article
    DOI: 10.1128/spectrum.00691-22
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 2807133-5
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  • 7
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    Pseudorhodobacter antarcticus sp. nov., isolated from Antarctic intertidal sandy sediment, and emended description of the genus Pseudorhodobacter Uchino et al. 2002 emend. Jung et al. 2012
    Microbiology Society ; 2013
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 63, No. Pt_3 ( 2013-03-01), p. 849-854
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 63, No. Pt_3 ( 2013-03-01), p. 849-854
    Abstract: A Gram-negative, aerobic, non-motile, pink-pigmented and rod-shaped strain, designated ZS3-33 T , was isolated from Antarctic intertidal sandy sediment. The strain grew optimally at 15 °C and with 1.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 20. It could not produce bacteriochlorophyll a . The predominant cellular fatty acid was C 18 : 1 ω7 c and the predominant respiratory quinone was Q-10. The major polar lipids were phosphatidylglycerol, phosphatidylcholine, two unidentified aminophospholipids and an unidentified aminolipid. Analyses of 16S rRNA gene sequences revealed that strain ZS3-33 T belonged to the genus Pseudorhodobacter , showing 97.4 % similarity to the type strain of Pseudorhodobacter ferrugineus and 95.3 % similarity to the type strain of Pseudorhodobacter aquimaris . Levels of gyrB gene sequence similarity between strain ZS3-33 T and the type strains of P. ferrugineus and P. aquimaris were 87.6 and 81.7 %, respectively. DNA–DNA relatedness between strain ZS3-33 T and P. ferrugineus DSM 5888 T was 56.6 %. The genomic DNA G+C content of strain ZS3-33 T was 57.1 mol%. Based on data from this polyphasic study, strain ZS3-33 T represents a novel species of the genus Pseudorhodobacter , for which the name Pseudorhodobacter antarcticus sp. nov. is proposed. The type strain is ZS3-33 T ( = CGMCC 1.10836 T  = KCTC 23700 T ). An emended description of the genus Pseudorhodobacter Uchino et al. 2002 emend. Jung et al. 2012 is also proposed.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijs.0.042184-0
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2013
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
    SSG: 12
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  • 8
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    Filamentous phages prevalent in Pseudoalteromonas spp. confer properties advantageous to host survival in Arctic sea ice
    Springer Science and Business Media LLC ; 2015
    In:  The ISME Journal Vol. 9, No. 4 ( 2015-4), p. 871-881
    Details
    In: The ISME Journal, Springer Science and Business Media LLC, Vol. 9, No. 4 ( 2015-4), p. 871-881
    Type of Medium: Online Resource
    ISSN: 1751-7362 , 1751-7370
    URL: Article
    DOI: 10.1038/ismej.2014.185
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
    detail.hit.zdb_id: 2299378-2
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  • 9
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    Vibrio algicola sp. nov., isolated from the surface of coralline algae
    Microbiology Society ; 2020
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 70, No. 9 ( 2020-09-01), p. 5149-5155
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 70, No. 9 ( 2020-09-01), p. 5149-5155
    Abstract: A Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic and rod-shaped bacterium, designated strain SM1977 T , was isolated from the surface of coralline algae collected from the intertidal zone at Qingdao, PR China. The strain grew at 10–35 °C, pH 4.5–8.5 and with 1–8.5% (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 20 and DNA. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1977 T was affiliated with the genus Vibrio , having the highest sequence similarity (97.6 %) to the type strain of Vibrio casei , followed by those of another five species (95.6–97.6 %) in the Rumoiensis clade of the genus Vibrio . However, the in silico DNA–DNA hybridization (75.3–75.9 %) and average nucleotide identity (21.6–22.8 %) values of SM1977 T against these close relatives were all below the corresponding thresholds to discriminate bacterial species. The major fatty acids were summed feature 3 (C 16:1  ω 7 c and/or C 16:1  ω 6 c ), C 16:0 and summed feature 8 (C 18:1  ω 6 c and /or C 18:1  ω 7 c ). The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The sole respiratory quinone was Q-8. The genomic DNA G+C content of strain SM1977 T , determined from the obtained whole genomic sequence, was 42.3 mol%. On the basis of the polyphasic results obtained in this study, strain SM1977 T is considered to represent a novel species within the genus Vibrio , for which the name Vibrio algicola sp. nov. is proposed. The type strain is SM1977 T (=MCCC 1K04351 T =KCTC 72847 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.004394
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2020
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 10
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    Structural basis and evolution of the photosystem I–light-harvesting supercomplex of cryptophyte algae
    Oxford University Press (OUP) ; 2023
    In:  The Plant Cell Vol. 35, No. 7 ( 2023-06-26), p. 2449-2463
    Details
    In: The Plant Cell, Oxford University Press (OUP), Vol. 35, No. 7 ( 2023-06-26), p. 2449-2463
    Abstract: Cryptophyte plastids originated from a red algal ancestor through secondary endosymbiosis. Cryptophyte photosystem I (PSI) associates with transmembrane alloxanthin-chlorophyll a/c proteins (ACPIs) as light-harvesting complexes (LHCs). Here, we report the structure of the photosynthetic PSI–ACPI supercomplex from the cryptophyte Chroomonas placoidea at 2.7-Å resolution obtained by crygenic electron microscopy. Cryptophyte PSI–ACPI represents a unique PSI–LHCI intermediate in the evolution from red algal to diatom PSI–LHCI. The PSI–ACPI supercomplex is composed of a monomeric PSI core containing 14 subunits, 12 of which originated in red algae, 1 diatom PsaR homolog, and an additional peptide. The PSI core is surrounded by 14 ACPI subunits that form 2 antenna layers: an inner layer with 11 ACPIs surrounding the PSI core and an outer layer containing 3 ACPIs. A pigment-binding subunit that is not present in any other previously characterized PSI–LHCI complexes, ACPI-S, mediates the association and energy transfer between the outer and inner ACPIs. The extensive pigment network of PSI–ACPI ensures efficient light harvesting, energy transfer, and dissipation. Overall, the PSI–LHCI structure identified in this study provides a framework for delineating the mechanisms of energy transfer in cryptophyte PSI–LHCI and for understanding the evolution of photosynthesis in the red lineage, which occurred via secondary endosymbiosis.
    Type of Medium: Online Resource
    ISSN: 1040-4651 , 1532-298X
    URL: Article
    DOI: 10.1093/plcell/koad087
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 623171-8
    detail.hit.zdb_id: 2004373-9
    SSG: 12
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