PXD007728

PXD007728 is an original dataset announced via ProteomeXchange.

Title	Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations
Description	High representation by ammonia-oxidizing archaea (AOA) in marine systems is consistent with their high affinity for ammonia, efficient carbon fixation, and copper (Cu)-centric respiratory system. However, little is known about their response to nutrient stress. We therefore used global transcriptional and proteomic analyses to characterize the response of a model AOA, Nitrosopumilus maritimus SCM1, to ammonia starvation, Cu limitation, and Cu excess. Most predicted protein-coding genes were transcribed in exponentially growing cells, and of ~74% detected in the proteome, ~6% were modified by N-terminal acetylation. The general response to ammonia starvation and Cu-stress was down-regulation of genes for energy generation and biosynthesis. Cells rapidly depleted transcripts for the A and B subunits of ammonia monooxygenase (AMO) in response to ammonia starvation, yet retained relatively high levels of transcripts for the C subunit. Thus, similar to ammonia-oxidizing bacteria, selective retention of amoC transcripts during starvation appears important for subsequent recovery, and also suggests that AMO subunit transcript ratios could be used to assess the physiological status of marine populations. Unexpectedly, cobalamin biosynthesis was upregulated in response to both ammonia starvation and Cu-stress, indicating the importance of this cofactor in retaining functional integrity during times of stress.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:40:24.881.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rachel Lundeen
SpeciesList	scientific name: Nitrosopumilus maritimus SCM1; NCBI TaxID: 436308;
ModificationList	mono N-acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-09-12 03:58:00	ID requested
1	2017-10-26 23:52:17	announced
⏵ 2	2024-10-22 04:40:25	announced	2024-10-22: Updated project metadata.

Qin W, Amin SA, Lundeen RA, Heal KR, Martens-Habbena W, Turkarslan S, Urakawa H, Costa KC, Hendrickson EL, Wang T, Beck DA, Tiquia-Arashiro SM, Taub F, Holmes AD, Vajrala N, Berube PM, Lowe TM, Moffett JW, Devol AH, Baliga NS, Arp DJ, Sayavedra-Soto LA, Hackett M, Armbrust EV, Ingalls AE, Stahl DA, Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations. ISME J, 12(2):508-519(2018) [pubmed]

10.1038/ismej.2017.186;

curator keyword: Biological

submitter keyword: marine ammonia oxidizing archaea,Nitrosopumilus maritimus (strain SCM1)

Anitra Ingalls
contact affiliation	University of Washington
contact email	aingalls@uw.edu
lab head
Rachel Lundeen
contact affiliation	University of Washington
contact email	ralundeen@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/10/PXD007728

PRIDE project URI

• PRIDE
  1. PXD007728
     1. Label: PRIDE project
     2. Name: Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations