PT - JOURNAL ARTICLE AU - Niederhuber, Matthew J. AU - Lambert, Talley J. AU - Yapp, Clarence AU - Silver, Pamela A. AU - Polka, Jessica K. TI - Super-resolution microscopy of the ß-carboxysome reveals a homogenous matrix AID - 10.1101/086090 DP - 2017 Jan 01 TA - bioRxiv PG - 086090 4099 - http://biorxiv.org/content/early/2017/01/29/086090.short 4100 - http://biorxiv.org/content/early/2017/01/29/086090.full AB - Carbon fixation in cyanobacteria makes a major contribution to the global carbon cycle. The cyanobacterial carboxysome is a proteinaceous microcompartment that protects and concentrates the carbon-fixing enzyme RuBisCO in a paracrystalline lattice, making it possible for these organisms to fix CO2 from the atmosphere. The protein responsible for the organization of this lattice in beta-type carboxysomes of the freshwater cyanobacterium Synechococcus elongatus, CcmM, occurs in two isoforms thought to localize differentially within the carboxysome matrix. Here we use widefield timelapse and 3D-structured illumination microscopy (3D-SIM) to study the recruitment and localization of these two isoforms. We demonstrate that this super-resolution technique is capable of successfully resolving the outer protein shell of the carboxysome from its internal cargo. We develop an automated analysis pipeline to analyze and quantify 3D-SIM images and generate a population level description of carboxysome shell protein, RuBisCO, and CcmM isoform localization. We find that both CcmM isoforms colocalize in space and time, prompting a revised model of the internal arrangement of the beta carboxysome.