{"entity": "researcher", "timestamp": "2026-08-23T09:27:05.446Z", "family": "Andersson", "given": "Siv G E", "initials": "SGE", "orcid": "0000-0003-0864-0259", "affiliations": ["Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, SE-751 24 Uppsala, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/6cfabb862b3544aa84cb14312670120c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/6cfabb862b3544aa84cb14312670120c"}}, "publications": [{"entity": "publication", "iuid": "3e8edb3e33e948c8998f80d5408ea729", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e8edb3e33e948c8998f80d5408ea729.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e8edb3e33e948c8998f80d5408ea729"}}, "title": "Origin and Evolution of Key Enzymes in the Anammox Pathway Revisited.", "authors": [{"family": "H\u00e4gglund", "given": "Emil", "initials": "E", "orcid": "0000-0002-0829-9882", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ea45b66a6854e919e97fcb6805fa45b.json"}}, {"family": "Jim\u00e9nez-Gonz\u00e1lez", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3493-4154", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c9c5183d3c84102badb256ed82ea16f.json"}}, {"family": "Hagstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Bj\u00f6rkholm", "given": "Patrik", "initials": "P", "orcid": "0000-0002-9131-4122", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/818d8b953fc34ae69a348517363d1ba2.json"}}, {"family": "Guy", "given": "Lionel", "initials": "L", "orcid": "0000-0001-8354-2398", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93e170c891c742838951a1fc8b50d223.json"}}, {"family": "Andersson", "given": "Siv G E", "initials": "SGE", "orcid": "0000-0003-0864-0259", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6cfabb862b3544aa84cb14312670120c.json"}}], "type": "journal article", "published": "2026-01-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "18", "issue": "1", "issn-l": "1759-6653"}, "abstract": "Anaerobic ammonium oxidizing bacteria in the class \"Candidatus Brocadiia\" in the Planctomycetota are the only known group of bacteria capable of producing energy by coupling the oxidation of ammonium to the reduction of nitrite within a unique bacterial organelle called the anammoxosome. Due to the lack of homologs in other species, it is hypothesized that the key enzyme in this process, the hydrazine synthase complex, originated by de novo birth. We performed extensive searches for proteins that exhibited similarity in sequence and structure to the hydrazine synthase subunits and identified distantly related homologs in anaerobic bacteria from the phyla Planctomycetota and Desulfobacterota. However, key residues of importance for the enzymatic function were not conserved, rejecting the hypothesis that the identified genes represent previously unrecognized anammox bacteria. Phylogenetic analyses indicate that the anammox pathway has been assembled from genes acquired by horizontal gene transfer from a variety of anaerobic bacteria. The ancestral states of enzymes in the hydroxylamine oxidoreductase family were inferred, and transitions between reductive and oxidative forms of the enzymes were mapped onto the phylogenetic tree. Finally, it is shown that the signal sequences of key enzymes in the anammox pathway are able to transport a reporter gene into the periplasm of Escherichia coli cells. In conclusion, our findings suggest that the hydrazine synthase complex has evolved from already existing heme-binding periplasmic proteins and that the anammoxosome has an endogenous origin.", "doi": "10.1093/gbe/evaf244", "pmid": "41410107", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12758564"}, {"db": "pii", "key": "8383170"}], "notes": [], "created": "2026-08-20T09:41:26.947Z", "modified": "2026-08-20T09:41:27.104Z"}, {"entity": "publication", "iuid": "78795f1ae417401a915a2d28fa43e74b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/78795f1ae417401a915a2d28fa43e74b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/78795f1ae417401a915a2d28fa43e74b"}}, "title": "Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota.", "authors": [{"family": "Odelgard", "given": "Anna", "initials": "A"}, {"family": "H\u00e4gglund", "given": "Emil", "initials": "E", "orcid": "0000-0002-0829-9882", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ea45b66a6854e919e97fcb6805fa45b.json"}}, {"family": "Guy", "given": "Lionel", "initials": "L", "orcid": "0000-0001-8354-2398", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93e170c891c742838951a1fc8b50d223.json"}}, {"family": "Andersson", "given": "Siv G E", "initials": "SGE", "orcid": "0000-0003-0864-0259", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6cfabb862b3544aa84cb14312670120c.json"}}], "type": "journal article", "published": "2024-04-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "4", "issn-l": "1759-6653"}, "abstract": "The recently isolated bacterium \"Candidatus Uabimicrobium amorphum\" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that \"Ca. Uabimicrobium amorphum\" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in \"Ca. Uabimicrobium amorphum\", of which 66 families contained eukaryotic-like Serine/Threonine kinases with Pkinase domains. In total, we predicted 525 functional Serine/Threonine kinases in \"Ca. Uabimicrobium amorphum\", which represent 8% of the proteome and is the highest fraction of Serine/Threonine kinases in a bacterial proteome. The majority of Serine/Threonine kinases in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the Serine/Threonine kinases of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the Serine/Threonine kinases in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the Serine/Threonine kinases in \"Ca. Uabimicrobium amorphum\". The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.", "doi": "10.1093/gbe/evae068", "pmid": "38547507", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11032199"}, {"db": "pii", "key": "7637138"}], "notes": [], "created": "2026-08-20T09:41:20.543Z", "modified": "2026-08-20T09:41:20.573Z"}, {"entity": "publication", "iuid": "73ce8aea453443a8809aebc9f24673f7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/73ce8aea453443a8809aebc9f24673f7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/73ce8aea453443a8809aebc9f24673f7"}}, "title": "TADA: taxonomy-aware dataset aggregator.", "authors": [{"family": "H\u00e4gglund", "given": "Emil", "initials": "E", "orcid": "0000-0002-0829-9882", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ea45b66a6854e919e97fcb6805fa45b.json"}}, {"family": "Andersson", "given": "Siv G E", "initials": "SGE", "orcid": "0000-0003-0864-0259", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6cfabb862b3544aa84cb14312670120c.json"}}, {"family": "Guy", "given": "Lionel", "initials": "L", "orcid": "0000-0001-8354-2398", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93e170c891c742838951a1fc8b50d223.json"}}], "type": "journal article", "published": "2023-12-01", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "39", "issue": "12", "issn-l": "1367-4803"}, "abstract": "The profusion of sequenced genomes across the bacterial and archeal domains offers unprecedented possibilities for phylogenetic and comparative genomic analyses. In general, phylogenetic reconstruction is improved by the use of more data. However, including all available data is (i) not computationally tractable, and (ii) prone to biases, as the abundance of genomes is very unequally distributed over the biological diversity. Thus, in most cases, subsampling taxa to build a phylogeny is necessary. Currently, though, there is no available software to perform that handily. Here we present TADA, a taxonomic-aware dataset selection workflow that allows sampling across user-defined portions of the prokaryotic diversity with variable granularity, while setting constraints on genome quality and balance between branches.\n\nTADA is implemented as a snakemake workflow and is freely available at https://github.com/emilhaegglund/TADA.", "doi": "10.1093/bioinformatics/btad742", "pmid": "38060257", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10733731"}, {"db": "pii", "key": "7461186"}], "notes": [], "created": "2026-08-20T09:39:42.007Z", "modified": "2026-08-20T09:39:42.135Z"}]}