Purple sulfur bacteria (PSB) convert light energy into chemical energy through photosynthesis. Interestingly, certain species can photosynthesize even in environments with low-calcium levels. Using cryo-electron microscopy, researchers from University of Tsukuba unveiled the structure of light-harvesting complexes and elucidated the mechanism that facilitates photosynthesis under low-calcium conditions.
Tsukuba, Japan—Photosynthetic bacteria, unlike plants, do not generate oxygen as a photosynthetic byproduct because they use hydrogen sulfide instead of water to convert solar energy into chemical energy (electrons). This process is orchestrated by a protein complex, the light-harvesting 1-reaction center (LH1-RC). Numerous PSB thrive in calcium-rich environments, such as hot springs and seawater. In the three-dimensional LH1-RC structure, the LH1 antenna protein is typically associated with calcium. However, the photosynthetic mechanism remains elusive in Allochromatium vinosum, a model species of autotrophic bacteria capable of thriving in low-calcium or soft-water environments, as hypothetically, calcium is not involved in the photosynthetic process in this model.
Using cryo-electron microscopy, the researchers revealed the LH1-RC structures of this model species at a resolution that enabled individual amino acid visualization. These observations revealed calcium binding only at six specific sites in the LH1 subunit. In contrast, the closely related thermophilic bacterium Thermochromatium tepidum displayed calcium attachment across all 16 LH1 subunits, indicating a calcium binding dependence on the amino acid sequence pattern. These results imply an evolutionary adaptation in this species, enabling it to bind trace amounts of calcium in low-calcium environments, thereby improving its thermal stability for photosynthesis.
These findings would potentially advance the efficient use of solar energy, and contribute to environmental protection, and highlight the capability of certain species to conduct photosynthesis in freshwater while detoxifying hydrogen sulfide, which is toxic to numerous organisms, into sulfur.
### This research was partially supported by Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Numbers JP21am0101118 and JP21am0101116, and JP23ama121004
Original Paper
Title of original paper:
High-Resolution Structure and Biochemical Properties of the LH1-RC Photocomplex from the Model Purple Sulfur Bacterium, Allochromatium vinosum
High performance computing is the basic technology needed to support today’s large scale scientific simulations. It covers a wide variety of issues on hardware and software for high-end computing such as high speed computation, high speed networking, large scale memory and disk storage, high speed numerical algorithms, programming schemes and the system softwares to support them. Current advanced supercomputer systems are based on large scale parallel processing systems. Nowadays, even application users are required to understand these technologies to a certain level for their effective utilization. In this class, we focus on the basic technology of high-end computing systems, programming, algorithm and performance tuning for application users who aim to use these systems for their practical simulation and computing.
Lecture Day and Location
Lecture Day:
February 21 (Wed), 22 (Thu), 2024
Location:
Online (Zoom link will be sent by email.)
Notice:
This intensive course will also be held as Korea-Japan HPC Winter School 2023.
Parallel processing systems (SMP, NUMA, Cluster, Grid, etc.), Memory hierarchy, Memory bandwidth, Network, Communication bandwidth, Delay.
Ryohei Kobayashi
3
Parallel Programming 1: OpenMP
Parallel programming model, parallel programming language OpenMP.
Akira Nukada
4
Parallel Programming 2: MPI
Parallel programming language MPI.
Norihisa Fujita
5
Parallel Numerical Algorithm 1
Krylov subspace iterative methods and their parallelization methods.
Hiroto Tadano
6
Parallel Numerical Algorithm 2
Fast Fourier Transformation (FFT) and its parallelization methods.
Daisuke Takahashi
7
Computation Optimization
Program optimization techniques (Register blocking, Cache blocking, Memory allocation, etc.) and performance evaluation on a compute node of parallel processing systems.
Daisuke Takahashi
8
GPU Computing
Introduction of GPU architecture and GPU programming.
東北大学加齢医学研究所の魏范研教授、Raja Norazireen Raja Ahmad研究員らは、熊本大学大学院生命科学研究部富澤一仁教授、筑波大学計算科学研究センター重田育照教授らとの共同研究により、可逆性小児肝不全患者で報告されている17種類のMTU1遺伝子変異の作用を明らかにしました。これらの変異はMTU1の酵素活性とタンパク量の低下を引き起こすことで、MTU1によるミトコンドリアtRNA硫黄修飾を大きく障害し、ミトコンドリアでのタンパク質翻訳とエネルギー代謝の低下原因となることがわかりました。