The transcriptomic landscape of Magnetospirillum gryphiswaldense during magnetosome biomineralization.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36217140", "kind": "science-record", "revision": 5, "content_hash": "sha256:111418ae3da70c9ec4fb181c17ce597b4ad82300edac5f7fa84c130053692ce4", "created_at": "2026-11-01T18:15:34Z", "updated_at": "2026-11-01T22:50:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The transcriptomic landscape of Magnetospirillum gryphiswaldense during magnetosome biomineralization.", "doi": "10.1186/s12864-022-08913-x", "pmid": "36217140", "authors": ["Cornelius N Riese", "Manuel Wittchen", "Valérie Jérôme", "Ruth Freitag", "Tobias Busche", "Jörn Kalinowski", "Dirk Schüler"], "journal": "BMC genomics", "year": 2022, "abstract": "BACKGROUND: One of the most complex prokaryotic organelles are magnetosomes, which are formed by magnetotactic bacteria as sensors for navigation in the Earth's magnetic field. In the alphaproteobacterium Magnetospirillum gryphiswaldense magnetosomes consist of chains of magnetite crystals (Fe3O4) that under microoxic to anoxic conditions are biomineralized within membrane vesicles. To form such an intricate structure, the transcription of > 30 specific structural genes clustered within the genomic magnetosome island (MAI) has to be coordinated with the expression of an as-yet unknown number of auxiliary genes encoding several generic metabolic functions. However, their global regulation and transcriptional organization in response to anoxic conditions most favorable for magnetite biomineralization are still unclear.\nRESULTS: Here, we compared transcriptional profiles of anaerobically grown magnetosome forming cells with those in which magnetosome biosynthesis has been suppressed by aerobic condition. Using whole transcriptome shotgun sequencing, we found that transcription of about 300 of the > 4300 genes was significantly enhanced during magnetosome formation. About 40 of the top upregulated genes are directly or indirectly linked to aerobic and anaerobic respiration (denitrification) or unknown functions. The mam and mms gene clusters, specifically controlling magnetosome biosynthesis, were highly transcribed, but constitutively expressed irrespective of the growth condition. By Cappable-sequencing, we show that the transcriptional complexity of both the MAI and the entire genome decreased under anaerobic conditions optimal for magnetosome formation. In addition, predominant promoter structures were highly similar to sigma factor σ70 dependent promoters in other Alphaproteobacteria.\nCONCLUSIONS: Our transcriptome-wide analysis revealed that magnetite biomineralization relies on a complex interplay between generic metabolic processes such as aerobic and anaerobic respiration, cellular redox control, and the biosynthesis of specific magnetosome structures. In addition, we provide insights into global regulatory features that have remained uncharacterized in the widely studied model organism M. gryphiswaldense, including a comprehensive dataset of newly annotated transcription start sites and genome-wide operon detection as a community resource (GEO Series accession number GSE197098).", "claims": [{"id": "claim-method", "statement": "The reads mapped to genes of three biological replicates per condition were counted by the implemented tool in the ReadXplorer software and tested for differential expression with DESeq2 [77] using default settings.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36217140", "locator": "sections[21] \"Differential gene expression analysis\" paragraph 2", "quote": "The reads mapped to genes of three biological replicates per condition were counted by the implemented tool in the ReadXplorer software and tested for differential expression with DESeq2 [77] using default settings."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE197098, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197098.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36217140", "locator": "sections[28] \"notes\" paragraph 1", "quote": "The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE197098, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197098."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using whole transcriptome shotgun sequencing, we found that transcription of about 300 of the > 4300 genes was significantly enhanced during magnetosome formation.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36217140", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Using whole transcriptome shotgun sequencing, we found that transcription of about 300 of the > 4300 genes was significantly enhanced during magnetosome formation."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using whole transcriptome shotgun sequencing, we found that transcription of about 300 of the > 4300 genes was significantly enhanced during magnetosome formation.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:36217140"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE197098"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE197098"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36217140", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12864-022-08913-x", "sha256": "sha256:a31ebe145e704bf487e5fd32520a9c5517c1e29499d3205171bc4e96ecc61ee2", "bytes": 55154, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12864-022-08913-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9549626", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE197098", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197098", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE197098", "version": null, "note": "The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE197098, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197098.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE197098, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197098.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5908637", "GSM5908638", "GSM5908639", "GSM5908640", "GSM5908641", "GSM5908642", "GSM5908643", "GSM5908644", "GSM5908645", "GSM5908646", "GSM5908647", "GSM5908648", "GSM5908649", "GSM5908650", "GSM5908651", "GSM5908652"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "29858", "taxon": "Magnetospirillum gryphiswaldense", "title": "The transcriptome of Magnetospirillum gryphiswaldense during magnetosome biomineralization", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE197098 not downloaded", "asset:data:geo:GSE197098 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The reads mapped to genes of three biological replicates per condition were counted by the implemented tool in the ReadXplorer software and tested for differential expression with DESeq2 [77] using default settings."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: deseq2."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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