title: Atomic force microscopy of photosystem II and its unit cell clustering quantitatively delineate the mesoscale variability in Arabidopsis thylakoids.
abstract: Photoautotrophic organisms efficiently regulate absorption of light energy to sustain photochemistry while promoting photoprotection. Photoprotection is achieved in part by triggering a series of dissipative processes termed non-photochemical quenching (NPQ), which depend on the re-organization of photosystem (PS) II supercomplexes in thylakoid membranes. Using atomic force microscopy, we characterized the structural attributes of grana thylakoids from Arabidopsis thaliana to correlate differences in PSII organization with the role of SOQ1, a recently discovered thylakoid protein that prevents formation of a slowly reversible NPQ state. We developed a statistical image analysis suite to discriminate disordered from crystalline particles and classify crystalline arrays according to their unit cell properties. Through detailed analysis of the local organization of PSII supercomplexes in ordered and disordered phases, we found evidence that interactions among light-harvesting antenna complexes are weakened in the absence of SOQ1, inducing protein rearrangements that favor larger separations between PSII complexes in the majority (disordered) phase and reshaping the PSII crystallization landscape. The features we observe are distinct from known protein rearrangements associated with NPQ, providing further support for a role of SOQ1 in a novel NPQ pathway. The particle clustering and unit cell methodology developed here is generalizable to multiple types of microscopy and will enable unbiased analysis and comparison of large data sets.
authors.affiliation: California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America.
authors.forename: Bibiana
authors.initials: B
authors.lastname: Onoa
authors.affiliation: Biophysics Graduate Group, University of California, Berkeley, California, United States of America.
authors.forename: Anna R
authors.initials: AR
authors.lastname: Schneider
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America; Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Brooks
authors.affiliation: Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America.
authors.forename: Patricia
authors.initials: P
authors.lastname: Grob
authors.affiliation: California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America; Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America; Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
authors.forename: Eva
authors.initials: E
authors.lastname: Nogales
authors.affiliation: California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America; Biophysics Graduate Group, University of California, Berkeley, California, United States of America; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America; Department of Chemistry, University of California, Berkeley, California, United States of America.
authors.forename: Phillip L
authors.initials: PL
authors.lastname: Geissler
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America; Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
authors.forename: Krishna K
authors.initials: KK
authors.lastname: Niyogi
authors.affiliation: California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America; Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America; Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America; Department of Physics, University of California, Berkeley, California, United States of America; Kavli Energy NanoSciences Institute at the University of California, Berkeley and the Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
authors.forename: Carlos
authors.initials: C
authors.lastname: Bustamante
mesh_terms: D017360:Arabidopsis / Q000378:metabolism / Q000648:ultrastructure*; D003460:Crystallization; D018625:Microscopy, Atomic Force; D045332:Photosystem II Protein Complex / Q000378:metabolism / Q000648:ultrastructure*; D021381:Protein Transport; D020524:Thylakoids / Q000378:metabolism / Q000648:ultrastructure*
chemical_list: D045332:Photosystem II Protein Complex