title: Cyanobacterial ultrastructure in light of genomic sequence data.
abstract: Cyanobacteria are physiologically and morphologically diverse photosynthetic microbes that play major roles in the carbon and nitrogen cycles of the biosphere. Recently, they have gained attention as potential platforms for the production of biofuels and other renewable chemicals. Many cyanobacteria were characterized morphologically prior to the advent of genome sequencing. Here, we catalog cyanobacterial ultrastructure within the context of genomic sequence information, including high-magnification transmission electron micrographs that represent the diversity in cyanobacterial morphology. We place the image data in the context of tabulated protein domains-which are the structural, functional, and evolutionary units of proteins-from the 126 cyanobacterial genomes comprising the CyanoGEBA dataset. In particular, we identify the correspondence between ultrastructure and the occurrence of genes encoding protein domains related to the formation of cyanobacterial inclusions. This compilation of images and genome-level domain occurrence will prove useful for a variety of analyses of cyanobacterial sequence data and provides a guidebook to morphological features.
authors.affiliation: MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.
authors.forename: C R
authors.initials: CR
authors.lastname: Gonzalez-Esquer
authors.affiliation: Department of Biology, Faculty of Medicine, Masaryk University, University Campus, Building A6, Kamenice 5, 625 00, Brno, Czech Republic.
authors.forename: J
authors.initials: J
authors.lastname: Smarda
authors.affiliation: Unité des Cyanobactéries, Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) Unité de Recherche Associée (URA) 2172, 75724, Paris Cedex 15, France.
authors.forename: R
authors.initials: R
authors.lastname: Rippka
authors.affiliation: Bioinformatics Graduate Group, University of California, San Francisco, CA, 94158, USA.
authors.forename: S D
authors.initials: SD
authors.lastname: Axen
authors.affiliation: Institut de Biologie de l'ENS, IBENS, Inserm, U1024, CNRS, UMR 8197, Ecole Normale Supérieure, 75005, Paris, France.
authors.forename: G
authors.initials: G
authors.lastname: Guglielmi
authors.affiliation: Unité des Cyanobactéries, Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) Unité de Recherche Associée (URA) 2172, 75724, Paris Cedex 15, France.
authors.forename: M
authors.initials: M
authors.lastname: Gugger
authors.affiliation: MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA. ckerfeld@lbl.gov.|Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. ckerfeld@lbl.gov.|Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA. ckerfeld@lbl.gov.|Berkeley Synthetic Biology Institute, UC Berkeley, Berkeley, CA, USA. ckerfeld@lbl.gov.|Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA. ckerfeld@lbl.gov.
authors.forename: C A
authors.identifier: http://orcid.org/0000-0002-9977-8482
authors.initials: CA
authors.lastname: Kerfeld
mesh_terms: D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D000458:Cyanobacteria / Q000235:genetics / Q000648:ultrastructure; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D046529:Microscopy, Electron, Transmission; D010802:Phylogeny; D000072417:Protein Domains; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins
keywords: Bioinformatics; Carboxysome; Cyanobacteria; Cyanophycin; Gas vesicles; Glycogen; Lipid droplets; Morphology; PHB; Polyphosphate; Protein domain; Transmission electron microscopy; Ultrastructure