DOI: 10.5061/dryad.2z34tmptf
title: Data from: Nitrogen fixing organelle in a marine alga

description: Symbiotic interactions were key to evolution of chloroplast and
 mitochondria organelles which mediate carbon and energy metabolism in
 eukaryotes. Biological nitrogen fixation, the reduction of abundant
 atmospheric nitrogen gas (N2) to biologically available ammonia is a key
 metabolic process performed exclusively by prokaryotes. UCYN-A is a
 metabolically streamlined N2-fixing cyanobacterium previously reported to
 be an endosymbiont of a marine unicellular alga. Here we show that UCYN-A
 has been tightly integrated into algal cell architecture and organellar
 division, and that it imports proteins encoded by the algal genome. These
 are characteristics of organelles and show that UCYN-A has evolved beyond
 endosymbiosis and functions as an early evolutionary stage N2-fixing
 organelle, or “nitroplast”.
description: # Data from: Nitrogen fixing organelle in a marine alga
 [https://doi.org/10.5061/dryad.2z34tmptf](https://doi.org/10.5061/dryad.2z34tmptf) ## Description of the data and file structure: ### SXT: 3-dimensional soft X-ray tomographic data generated by the National Center for X-ray Tomography (ncxt.org). Each file represents one or more cells of *B. bigelowii*-UCYN-A complex. Files are in the MRC file format. File details below. Cell identification: * Zehr_UCYNA_FR12_fission_xxx_xxx:= data showing two UCYN-A with relative alteration of host cell's structural features (mitochondrial network, nucleus, plastids) * Zehr_UCYNA_FR12_cytokinesis_xxx_xxx:= data showing the process of the cytokinesis of doubling cells * Zehr_UCYNA_FR12_growth_xxx_xxx:= data showing the process of cell's growth and reorganization after cytokinesis * Zehr_UCYNA_FR12_L0_xxx_xxx:= data showing cell's architecture at L0 (cells harvested at 9 am) * Zehr_UCYNA_FR12_L6_xxx_xxx:= data showing cell's architecture at L6 (cells harvested at 3 pm) * Zehr_UCYNA_FR12_L12_xxx_xxx:= data showing cell's architecture at L6 (cells harvested at 9 pm) * Zehr_UCYNA_FR12_D6_xxx_xxx:= data showing cell's architecture at L6 (cells harvested at 3 am) Voxel size (nm): * Zehr_UCYNA_FR21_cytokinesis_3_10 35 * Zehr_UCYNA_FR21_cytokinesis_3_21 42 * Zehr_UCYNA_FR21_cytokinesis_2267_16 30 * Zehr_UCYNA_FR21_cytokinesis_2267_36 34 * Zehr_UCYNA_FR21_fission_6_3 30 * Zehr_UCYNA_FR21_fission_8_4 37 * Zehr_UCYNA_FR21_fission_8_13 43 * Zehr_UCYNA_FR21_fission_8_15 43 * Zehr_UCYNA_FR21_fission_8_20 43 * Zehr_UCYNA_FR21_fission_9_5 34 * Zehr_UCYNA_FR21_fission_9_8 34 * Zehr_UCYNA_FR21_fission_10_5 38 * Zehr_UCYNA_FR21_fission_1473_6 37 * Zehr_UCYNA_FR21_fission_1497_15 42 * Zehr_UCYNA_FR21_fission_2259_18 30 * Zehr_UCYNA_FR21_growth_3_20 42 * Zehr_UCYNA_FR21_growth_9_16 43 * Zehr_UCYNA_FR21_growth_11_4 30 * Zehr_UCYNA_FR21_growth_1497_7 33 * Zehr_UCYNA_FR21_growth_1497_8 33 * Zehr_UCYNA_FR21_L0_11_1 30 * Zehr_UCYNA_FR21_L0_24_3 37 * Zehr_UCYNA_FR21_L0_26_4 38 * Zehr_UCYNA_FR21_L0_30_6 34 * Zehr_UCYNA_FR21_L0_1457_10 30 * Zehr_UCYNA_FR21_L0_1457_11 30 * Zehr_UCYNA_FR21_L0_1_8 43 * Zehr_UCYNA_FR21_L0_3_5 35 * Zehr_UCYNA_FR21_L6_2_5 43 * Zehr_UCYNA_FR21_L6_4_16 38 * Zehr_UCYNA_FR21_L6_6_4 43 * Zehr_UCYNA_FR21_L6_8_1 30 * Zehr_UCYNA_FR21_L6_22_5 43 * Zehr_UCYNA_FR21_L6_22_7 43 * Zehr_UCYNA_FR21_L12_10_6 42 * Zehr_UCYNA_FR21_L12_10_9 43 * Zehr_UCYNA_FR21_L12_13_4 42 * Zehr_UCYNA_FR21_L12_13_8 43 * Zehr_UCYNA_FR21_L12_19_6 35 * Zehr_UCYNA_FR21_L12_19_10 38 * Zehr_UCYNA_FR21_D6_15_4 42 * Zehr_UCYNA_FR21_D6_15_7 43 * Zehr_UCYNA_FR21_D6_16_5 38 * Zehr_UCYNA_FR21_D6_16_8 42 * Zehr_UCYNA_FR21_D6_16_9 42 * Zehr_UCYNA_FR21_D6_16_12 42 ### Proteomics: 1\. Datasets S1-S7, protein quantifications in all samples, and protein database.  Datasets S1-S7 and protein quantifications are .csv files. * Data S1. (Data_S1_Bbigelowii_proteins.csv): Details of principal *B. bigelowii* localized proteins. * Data S2. (Data_S2_UCYN-A_proteins.csv): Details of principal UCYN-A encoded proteins. * Data S3. (Data \_S3_Biosynthesis.csv): Details of biosynthesis-related proteins * Data S4. (Data \_S4_Diazotrophy_related.csv): Details of diazotrophy and antioxidant-related proteins * Data S5. (Data \_S5_Ferredoxin_and_flavodox.csv): Details of *B. bigelowii* and UCYN-A encoded ferredoxins and flavodoxins. * Data S6. (Data \_S6_Regulatory_etc.csv): Details of regulatory proteins * Data S7. (Data_S7_Fig3Ainfo.xlsx): Details and abbreviations of proteins mentioned in Fig. 3A. * Column headings for S1-S7: detected in proteomes? = Yes if the protein was detected in any proteomic sample; uTP? = Yes if uTP sequence was detected using HMM approach; Enriched in whole-cell or UCYN-A samples, DESeq2 Wald test, P&lt;0.05 = identifies sample type in which protein is more abundant; Log2FC UCYN-A vs *B. bigelowii* samples (positive = UCYN-A) = gives log base 2 fold change between sample types with positive values indicating increased abundance in UCYN-A samples; Average quantity = average protein quantity (area-under-curve of the mass spectrometric peaks of all assigned peptides) in all triplicate samples. 2\. ADK1075_proteomics_DB_2.fasta fasta file containing all predicted *B. bigelowii* and UCYN-A proteins. These are generated from the UCYN-A2 genome (NCBI RefSeq GCF 020885515.1), *B. bigelowii* transcriptome (DDBJ/Genbank/ENA DRA011134), and *B. bigelowii* plastid genome (Genbank OR912953, OR912954 and OR912955) 3.ADK1075_ProteinQuantifications.csv contains protein quantification data for all proteins in all samples. Log2 fold change (positive = UCYN-A) and P values are calculated between UCYN-A and whole culture samples day and night using DESeq2 Wald test. The Sequence source column gives the origin of the sequence as either previously published *B. bigelowii* transcriptomes, previously published UCYN-A2 genome, *B. bigelowii* chloroplast genome (sequenced for this work), or contaminants. 4.UCYNA2_genome_description.csv gives functional annotations of the UCYN-A2 genome from 10.3389/fpls.2021.749895 5.Bbigelowii_transcriptome_annotations.csv gives functional annotations of the *B. bigelowii* transcriptomes from 10.3389/fpls.2021.749895 6.uTP_HMM_hits.fasta fasta file containing *B. bigelowii* protein sequences retrieved with our HMM search of ADK1075_proteomics_DB_2.fasta 7.Import_candidates.fasta fasta file containing all B. bigelowii protein sequences predicted to localize to UCYN-A, either by HMM detection of uTP,  significant enrichment in protein, or both ## Version changes **23-apr-2024:** Added additional columns to the ADK1075_ProteinQuantifications.csv file to clarify genomic origins of proteins detected, and added results of statistical tests for all proteins. Added files Bbigelowii_transcriptome_annotations.csv and UCYNA2_genome_descriptions.csv which give functional annotations of *B. bigelowii* and UCYN-A proteins. Added uTP_HMM_hits.fasta which includes all protein sequences determined to contain a uTP sequence by our HMM search. **26-apr-2024:** Added Import_candidates.fasta which contains protein sequences for all *B. bigelowii* proteins predicted to localize to UCYN-A by either HMM detection of uTP, significant enrichment in protein, or both. **24-jun-2024:** Updated column N in ADK1075_ProteinQuantifications.csv, which was miscalculated.