RT Journal Article SR Electronic T1 Super-resolution microscopy of the ß-carboxysome reveals a homogenous matrix JF bioRxiv FD Cold Spring Harbor Laboratory SP 086090 DO 10.1101/086090 A1 Matthew J. Niederhuber A1 Talley J. Lambert A1 Clarence Yapp A1 Pamela A. Silver A1 Jessica K. Polka YR 2016 UL http://biorxiv.org/content/early/2016/11/23/086090.abstract 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.