Browse
Submit Data
Databases
API
Help

Dataset Information

278 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic and proteomic responses of the oceanic diatom Pseudo-nitzschia granii to iron limitation

ABSTRACT: The oceanic diatom Pseudo-nitzschia granii was cultured in the laboratory under steady-state iron-replete and iron-limited conditions. Transcriptomic and proteomic analyses were performed to determine how this organism reorganizes major metabolic processes as a function of iron supply.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Pseudo-nitzschia Granii

SUBMITTER: Natalie Cohen

LAB HEAD: Mak A. Saito

PROVIDER: PXD009698 | Pride | 2018-08-21

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Transcriptomic and proteomic responses of the oceanic diatom Pseudo-nitzschia granii to iron limitation.

Cohen Natalie R NR Gong Weida W Moran Dawn M DM McIlvin Matthew R MR Saito Mak A MA Marchetti Adrian A

Environmental microbiology 20180801 8

Diatoms are a highly successful group of photosynthetic protists that often thrive under adverse environmental conditions. Members of the genus Pseudo-nitzschia are ecologically important diatoms which are able to subsist during periods of chronic iron limitation and form dense blooms following iron fertilization events. The cellular strategies within diatoms that orchestrate these physiological responses to variable iron concentrations remain largely uncharacterized. Using a combined transcript ...[more]

PMID: 30117243

Similar Datasets

Flexible B12 ecophysiology of Phaeocystis antarctica due to a B12-independent methionine synthase fusion protein with widespread homologues

Project description:Coastal Antarctic marine ecosystems play an important role in carbon cycling due to their highly productive seasonal phytoplankton blooms. Southern Ocean microbes are primarily limited by light and iron (Fe) and can be co-limited by cobalamin (vitamin B12 ). Micronutrient limitation is a key driver of ecosystem dynamics and influences the composition of blooms, which are often dominated by either diatoms or the haptophyte Phaeocystis antarctica, each with varied impacts on carbon cycling. However, the vitamin requirements and ecophysiology of the keystone species P. antarctica remains poorly characterized. Using cultures, physiological analysis, and comparative ’omics we examined the response of P. antarctica to a matrix of Fe-B12 conditions. We show that P. antarctica is not auxotrophic for B12 , as previously suggested, and report new mechanistic insights of its B12 response in cultures of predominantly solitary and colonial cells. Proteomics coupled with proteogenomics detected a B12 -independent methionine synthase fusion protein (MetE-fusion) that is expressed under vitamin limitation and is interreplaced with the B12 -dependent isoform (MetH) in replete conditions. Database searches returned homologs of the MetE-fusion protein in multiple Phaeocystis species and in a wide range of marine microbes, including other photosynthetic eukaryotes with polymorphic life cycles and also bacterioplankton. Furthermore, MetE-fusion homologs were found to be expressed in metaproteomic and metatranscriptomic field samples in polar and more geographically widespread regions. As climate change impacts micronutrient availability in the coastal Southern Ocean, our finding that P. antarctica has a flexible B12 metabolism has implications for its relative fitness compared to B12 -auxotrophic diatoms.

2023-02-27 | PXD031524 | Pride

Model Bacteria Physiological Studies Dataset 1: Triplicate replete proteomes for Ruergeria pomeroyi DSS-3 Dataset 2: Triplicate replete proteomes for Alteromonas macleodii MIT1002

Project description:These datasets represent the global proteome of biological triplicates of replete cultures of Ruergeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 (three samples each). These datasets are an initial examination of the proteome allocation of these two heterotrophic bacteria. 2341 and 2075 proteins were identified in DSS-3 and MIT1002, respectively.

2022-06-10 | PXD034365 | Pride

Pacific Ocean metaproteomics, METZYME KM1128

Project description:Global metaproteomic analyses of microbial biomass from the upper water column of the Central Pacific Ocean. This dataset was used as a discovery dataset to identify peptide biomarkers for cyanobacterial populations for use in targeted metaproteomic calibrated multiple reaction monitoring (MRM) analyses published in in Saito et al., 2014 and 2015. Saito, M. A., McIlvin, M. R., Moran, D. M., Goepfert, T. J., DiTullio, G. R., Post, A. F., and Lamborg, C. H.: Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers, Science, 345, 1173-1177, 2014. Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M., Rappé, M. S., DiTullio, G., and Moran, D.: Needles in the Blue Sea: Sub‐Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome, PROTEOMICS, 15, 3521-3531, 2015.

2019-02-12 | PXD009712 | Pride

Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

Project description:In this study, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic and UV light-induced stress and low dissolved pCO2. Additionally, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the metabolic response of N. marina to low (5.6 µM) O2 concentrations. In response to O2-limited conditions, the abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb3-type terminal oxidase increased, suggesting a role in sustaining nitrite oxidation-driven autotrophy under O2 limitation.

2021-04-20 | PXD021606 | Pride

RNA-seq of sexually reproducing Pseudo-nitzschia multistriata diatom cells

Project description:Biological relevance and intent of the experiment: Given their abundance in the oceans and the exceptional adaptive capacities that make them capable of colonizing the most disparate habitats, diatoms constitute a group of microalgae of considerable ecological importance. This experiment aims to provide a molecular characterization of sexual reproduction for the diatom Pseudo-nitzschia multistriata, in relation to the consumption of nutrients and the impact on the marine ecosystem, by exploring the gene expression changes occurring at different time points in the cells involved in the process. Experimental workflow: Cell cultures of P. multistriata belonging to opposite mating types (MT- and MT+) were grown in 12L/12D cycles at 18°C under normal light conditions (60 uE) and crossed at a final cell density of 20.000 cells/ml using half volume from each MT. Samples for transcriptomic analyses were collected at three time points for sexually reproducing cells (1 hour: T1, 24 hours: T2 and 120 hours: T3), and at one time point (24 hours: T2) for parental monocultures grown in parallel as control condition.

2021-11-24 | E-MTAB-8854 | biostudies-arrayexpress

Gene expression changes at the onset of sexual reproduction in the marine planktonic diatom Pseudo-nitzschia multistriata

Project description:Cultures of two Pseudo-nitzschia multistriata strains of opposite mating type were placed in a bipartite glass apparatus with a membrane separating them. This allows perception of sexual cues. Samples were taken at 2 hours and 6 hours from the start of the experiment and gene expression was compared to the same strains grown in monocultures.

2017-05-04 | E-MTAB-5469 | biostudies-arrayexpress

Dynamic metabolic efficiency of substrate utilization by copiotrophic marine bacteria

Project description:Under well-defined laboratory conditions, we grew R. pomeroyi DSS-3 and A. macleodii MIT1002 in batch cultures on a monosaccharide (glucose) and organic acid (acetate), provided either individually or in combination, and all at the same carbon equivalent. This batch culturing approach mimicked bacterial DOC assimilation in short-lived substrate ‘hot spots’, such as those formed by high phytoplankton extracellular release at peak photon availability. Measurements were made of bacterial metabolite uptake, respiration, and biomass accumulation through a growth cycle. Insights into bacterial core metabolism came from gene and protein expression measured at intervals during growth. Curated genome-scale models (flux balance analysis; FBA) were used to explore the metabolic foundation of CO2 production for insights into determinants of BGE and bCUE.

2023-10-27 | PXD045824 | Pride

Diel proteomes of field Trichodesmium populations

Project description:Diel proteomes of Trichodesmium colonies sampled from the field on March 10, 2018 from the Eastern subtropical Atlantic at 65 22.420W 17 0.284 N. These proteomes inform a broad study of diel proteome oscillations in Trichodesmium that support simultaneous photosynthesis and nitrogen fixation during the day.

2021-11-25 | PXD027796 | Pride

Lack of a Zn/Co substitution ability in the polar diatom Chaetoceros RS19

Project description:Functional substitution of the essential trace metals zinc (Zn) and cobalt (Co) within metalloenzymes has been well documented in marine diatoms and is known to be prevalent among varying genera and species. In contrast to the majority of species studied to date, we find that the polar diatom Chaetoceros RS19, originally isolated from the Ross Sea, Antarctica, has a Zn requirement that cannot be met by Co and thus does not demonstrate a Zn/Co substitution ability as assessed by growth rate. We investigate the underlying metabolic basis of Zn/Co substitution at the transporter, sensor/chaperone, and metalloenzyme level by employing metal quota, metal uptake rate, and proteomic analyses of this substitution-incapable diatom. Co appears to be transported into the cell, but not efficiently utilized by Zn metalloenzymes.

2022-03-02 | PXD026895 | Pride

The proteomic response of a marine Vibrio to low iron and desferrioxamine siderophore bioavailability

Project description:Competition for limited iron resources is a key driver of microbial community structure in many regions of the surface ocean. The bacterial siderophores ferrioxamine and amphibactin have been identified in marine surface waters, suggesting that they may represent an important bacterial strategy for obtaining iron from a scarcely populated pool. We screened several strains of marine Vibrio for the presence of putative amphibactin biosynthesis gene homologues and amphibactin production. Whole cell proteomics, siderophore isolation, and isotopically labeled iron uptake experiments were performed. Here, we show that an amphibactin-producing marine bacterium, Vibrio cyclitrophicus str. 1F-53, harbors an independently regulated uptake pathway for ferrioxamines. Proteomic analyses identified upregulation of the amphibactin NRPS system and a putative amphibactin siderophore transporter in response to low iron concentrations. In addition, multiple other transporters were upregulated, however when desferrioxamine was present, amphibactin production decreased and the ferrioxamine receptor increased in abundance. Such cheating phenotypes, which appear widespread among marine amphibactin producers, highlight the strategies that contribute to the fitness of marine bacteria in the face of iron stress. These results demonstrate siderophore producer and cheater phenotypes and highlight the cellular restructuring which is involved due to competition for iron, that shapes the community structure of marine ecosystems.

2021-04-19 | PXD011427 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data