PXD007174-3

PXD007174 is an original dataset announced via ProteomeXchange.

Title	Metaproteomics of viral concentrates at deep chlorophyll maximum of Scouth China Sea
Description	Marine viral concentrates (VCs) contains a substantial amount of non-cellular biological particles, e.g. viruses, gene transfer agents (GTAs) and membrane vesicles that are ecological significant. Metagenomic sequencing of VCs has been extensively applied to study the diversity and function potential of natural virions whereas information of nonn-viral components are often excluded for investigation. Here we apply a shotgun proteomic approach to characterize the origin and function of proteins in the VCs collected from the deep chlorophyll maximum (DCM) of the South China Sea. Using a custom database, we identified 636 non-redundant proteins represented by a total of 7220 spectra from the two VC samples. Cyanophages, pelagiphages, Phycodnaviridae and a group of uncultured viruses (previouly collected from DCM of Mediterranean Sea) contributed the most in the viral proteome. Seldom proteins related to RNA viruses and known GTAs were found despites of the presence of their sequences in the protein-searching database, suggested that these particles might be low abundant in the samples. Over 60% of identified spectra could not be assigned to viruses. The non-viral spectra were dominated by microbial groups of SAR324, SAR11, Actinobacteria and picoeukaryotic algae such as prasinophytes.Interestingly, we found that periplasmic proteins such as diverse ABC and TRAP transporters, and 56 kDa selenium-binding proteins, were enriched in this fraction.Together with other detected non-viral proteins,we could identify significant microbial functions, such as the utilization of glycine betaine, 3-dimethylsulphoniopropionate,and taurine by SAR11,and urea by prochlorococcus, nitrous oxide production by ammonia-oxidizing archaea and peroxide detoxification by unkonwn gammaproteobacteria. Our study of marine VCs demonstrates the potential application of metaproteomics to link the nano-size materials to the diversity of virions and interesting microbial functions in the ocean.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:49:25.865.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhangxian Xie
SpeciesList	scientific name: environmental samples ; NCBI TaxID: 151659;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-08-02 06:39:08	ID requested
1	2018-05-02 10:57:48	announced
2	2018-05-02 23:49:55	announced	Updated publication reference for PubMed record(s): 28925544.
⏵ 3	2023-11-14 08:49:26	announced	2023-11-14: Updated project metadata.

Xie ZX, Chen F, Zhang SF, Wang MH, Zhang H, Kong LF, Dai MH, Hong HS, Lin L, Wang DZ, Metaproteomics of marine viral concentrates reveals key viral populations and abundant periplasmic proteins in the oligotrophic deep chlorophyll maximum of the South China Sea. Environ Microbiol, 20(2):477-491(2018) [pubmed]

curator keyword: Metaproteomics

submitter keyword: virua, 56 kDa selenium-binding protein,viral concentrates, metaproteomics

Da-Zhi Wang
contact affiliation	State Key Laboratory of Marine Environmental Science / College of the Environment and Ecology, Xiamen University, China
contact email	dzwang@xmu.edu.cn
lab head
Zhangxian Xie
contact affiliation	State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, China
contact email	xiezhangxian@163.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD007174
     1. Label: PRIDE project
     2. Name: Metaproteomics of viral concentrates at deep chlorophyll maximum of Scouth China Sea