SPIRE-a software tool for bicontinuous phase recognition: application for plastid cubic membranes.

Abstract

Bicontinuous membranes in cell organelles epitomize nature's ability to create complex functional nanostructures. Like their synthetic counterparts, these membranes are characterized by continuous membrane sheets draped onto topologically complex saddle-shaped surfaces with a periodic network-like structure. Their structure sizes, (around 50-500 nm), and fluid nature make transmission electron microscopy (TEM) the analysis method of choice to decipher their nanostructural features. Here we present a tool, Surface Projection Image Recognition Environment (SPIRE), to identify bicontinuous structures from TEM sections through interactive identification by comparison to mathematical "nodal surface" models. The prolamellar body (PLB) of plant etioplasts is a bicontinuous membrane structure with a key physiological role in chloroplast biogenesis. However, the determination of its spatial structural features has been held back by the lack of tools enabling the identification and quantitative analysis of symmetric membrane conformations. Using our SPIRE tool, we achieved a robust identification of the bicontinuous diamond surface as the dominant PLB geometry in angiosperm etioplasts in contrast to earlier long-standing assertions in the literature. Our data also provide insights into membrane storage capacities of PLBs with different volume proportions and hint at the limited role of a plastid ribosome localization directly inside the PLB grid for its proper functioning. This represents an important step in understanding their as yet elusive structure-function relationship.

Plant phenotyping relevance

植物エチオプラストの膜構造をTEM画像から同定・定量解析するソフトウェアを開発し、植物器官の構造形質を抽出しているため、フェノタイピング手法が中心である。

Code and data availability

The paper's computational analysis tool SPIRE (used to identify and quantify prolamellar body cubic membrane structures from TEM micrographs) is explicitly released as open-source code with public URLs (SourceForge project and GitHub source repository), plus a video tutorial hosted at chloroplast.pl. No public deposit,