Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes
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PROVIDER: PRJNA850440 | ENA |
REPOSITORIES: ENA
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Project description:Although N2 fixation can occur in free-living cyanobacteria, the unicellular endosymbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is considered to be a dominant N2-fixing species in marine ecosystems. Four UCYN-A sublineages are known from partial nitrogenase (nifH) gene sequences. However, few studies have investigated their habitat preferences and regulation by their respective hosts in open-ocean versus coastal environments. Here, we compared UCYN-A transcriptomes from oligotrophic open-ocean versus nutrient-rich coastal waters. UCYN-A1 metabolism was more impacted by habitat changes than UCYN-A2. However, across habitats and sublineages genes for nitrogen fixation and energy production were highly transcribed. Curiously these genes, critical to the symbiosis for the exchange of fixed nitrogen for fixed carbon, maintained the same schedule of diel expression across habitats and UCYN-A sublineages, including UCYN-A3 in the open-ocean transcriptomes. Our results undersore the importance of nitrogen fixation in UCYN-A symbioses across habitats, with consequences for community interaction and global biogeochemical cycles.
2023-02-23 | GSE206403 | GEO
Project description:Decades of research on marine N2 fixation focused on Trichodesmium, which are generally free-living cyanobacteria, but in recent years the endosymbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) has received increasing attention. However, few studies have shed light on the influence of the host versus the habitat on UCYN-A N2 fixation and overall metabolism. Here we compared transcriptomes from natural populations of UCYN-A from oligotrophic open-ocean versus nutrient-rich coastal waters, using a microarray that targets the full genomes of UCYN-A1 and UCYN-A2 and known genes for UCYN-A3. We found that UCYN-A2, usually regarded as adapted to coastal environments, was transcriptionally very active in the open ocean and appeared to be less impacted by habitat change than UCYN-A1. Moreover, for genes with 24 h periodic expression we observed strong but inverse correlations among UCYN-A1, A2, and A3 to oxygen and chlorophyll, which suggests distinct host-symbiont relationships. Across habitats and sublineages, genes for N2 fixation and energy production had high transcript levels, and, intriguingly, were among the minority of genes that kept the same schedule of diel expression. This might indicate different regulatory mechanisms for genes that are critical to the symbiosis for the exchange of nitrogen for carbon from the host. Our results underscore the importance of N2 fixation in UCYN-A symbioses across habitats, with consequences for community interactions and global biogeochemical cycles.
| S-EPMC10153697 | biostudies-literature
Project description:Protein phosphorylation is an important post translational modification that plays a major role in cellular regulatory processes in both eukaryotes and prokaryotes. In recent years, aided by advancements in mass spectrometry techniques, there has been a growing interest in studying protein phosphorylation in prokaryotic model organisms. There are, however, only a limited number of phosphoproteomics reports on non-model organisms. Here, using mass spectrometry, we performed a genome wide investigation of protein phosphorylation in the non-model organism and biofuel producer Zymomonas mobilis under anaerobic, aerobic, and N2-fixing conditions. Our phosphoproteome analysis revealed 125 unique phosphorylated proteins and 172 unique phosphopeptides across these three growth conditions. The phosphoproteins identified belonged to major pathways, including glycolysis, TCA cycle, protein biosynthesis, electron transport, and nitrogen fixation. Quantitative analysis revealed significant and widespread changes in protein phosphorylation across anaerobic, aerobic, and N2-fixing growth conditions. For example, two different serine residues of KDPG aldolase, an Entner-Doudoroff pathway enzyme, were differentially phosphorylated under aerobic and N2-fixing conditions. On the other hand, the final enzyme in the ethanol fermentation pathway, alcohol dehydrogenase, showed phosphorylation on its Ser99 only under N2-fixing condition while its Ser126 was only phosphorylated under anaerobic condition. Moreover, nitrogenases and nitrogen regulatory proteins were differentially phosphorylated at multiple sites under aerobic and N2-fixing conditions. Altogether, this study provides new knowledge regarding potential phosphorylation regulatory sites of specific proteins in pathways relevant to ethanol production and overall physiology and establishes new ground for future engineering of Z. mobilis for advanced biofuel production.
2019-08-08 | PXD014065 | Pride
Project description:We herein conducted high throughput analyses of proteome and protein acetylation in Z. mobilis under N2-fixing conditions, and established its first acetylome.
2021-11-03 | PXD027418 | Pride
Project description:Phosphate limitation intensifies negative effects of ocean acidification on globally important nitrogen fixing cyanobacterium
| PRJNA751977 | ENA
Project description:Investigation of whole genome gene expression level changes in Trichodesmium erythraeum IMS101 during a 24-hr light and dark cycle. The diel gene expression analyzed in this study is further described in Muñoz-Marin, M., I. N. Shilova, T. Shi, H. Farnelid & J. P. Zehr. 2019. The transcriptional cycle is suited to daytime N2 fixation in the unicellular cyanobacterium “Candidatus Atelocyanobacterium thalassa” (UCYN-A). mBio 10:e02495-18. https://doi.org/10.1128/mBio.02495-18.
2017-06-11 | GSE99896 | GEO
Project description:For the filamentous cyanobacterium Anabaena variabilis to grow without combined nitrogen, certain cells differentiate into heterocysts that fix N2, while vegetative cells perform photosynthesis. Much remains unknown on how heterocysts differ from vegetative cells in terms of carbon and energy metabolisms. Microarrays were used to investigate gene transcription patterns in vegetative cells, heterocysts, and filaments of N2-fixing phototrophic, mixotrophic, and heterotrophic cultures.
2013-11-01 | GSE46076 | GEO
Project description:Investigation of whole genome gene expression level changes in two strains of the cyanobacteria Atelocyanobacterium thalasaa (UCYN-A) from environmental samples. The diel gene expression analyzed in this study is further described in Muñoz-Marin, M., I. N. Shilova, T. Shi, H. Farnelid & J. P. Zehr. 2017. Unicellular cyanobacterial symbiosis facilitates aerobic nitrogen fixation. Science (to be submitted).
2018-12-05 | GSE100124 | GEO
Project description:The filamentous diazotrophic cyanobacteria Trichodesmium spp. supply fixed nitrogen (N) to the N-depleted oligotrophic oceans where their growth is often limited by the low availability of phosphorus(P) and/or iron. Previous studies have mostly been focused on the effects of ocean acidification on Trichodesmium under nutrient sufficient or iron-limited conditions. Only a few studies have examined the impacts of ocean acidification on Trichodesmium grown at low P concentrations using non-steady-state batch cultures. Here we cultured Trichodesmium using P-limited continuous cultures (chemostat) to mimic steady-state oceanic low P condition, and used comparative NGS-derived Trichodesmium transcriptome profiling (RNA-seq) analysis to find differentially expressed genes and cellular pathways in response to acidification.
2022-10-13 | GSE181428 | GEO
Project description:Nitrogen-fixing microorganisms (diazotrophs) are keystone species that reduce atmospheric dinitrogen (N2) gas to fixed nitrogen (N), thereby accounting for much of N-based new production annually in the oligotrophic North Pacific. However, current approaches to study N2 fixation provide relatively limited spatiotemporal sampling resolution; hence, little is known about the ecological controls on these microorganisms or the scales over which they change. In the present study, we used a drifting robotic gene sensor to obtain high-resolution data on the distributions and abundances of N2-fixing populations over small spatiotemporal scales. The resulting measurements demonstrate that concentrations of N2 fixers can be highly variable, changing in abundance by nearly three orders of magnitude in less than 2 days and 30 km. Concurrent shipboard measurements and long-term time-series sampling uncovered a striking and previously unrecognized correlation between phosphate, which is undergoing long-term change in the region, and N2-fixing cyanobacterial abundances. These results underscore the value of high-resolution sampling and its applications for modeling the effects of global change.
| S-EPMC4030237 | biostudies-literature