Biology subjects

Kanno, R.

Publications and source records attributed to Kanno, R..

3 recordsLinked to original sources

bioRxiv2021

A Novel Membrane Protein in the Rhodobacter sphaeroides LH1-RC Photocomplex

We present a cryo-EM structure of the monomeric light-harvesting-reaction center (LH1-RC) core complex from photosynthetic purple bacterium Rhodobacter (Rba.) sphaeroides at 2.9 [A] resolution. The LH1 complex forms a C-shaped structure composed of 14 {beta}-polypeptides around the RC with a large ring opening. From the cryo-EM density map, a previously unrecognized integral membrane protein, referred to as protein-U, was identified. Protein-U has a U-shaped conformation near the LH1-ring opening and was annotated as a hypothetical protein in the Rba. sphaeroides genome. Deletion of protein-U resulted in a mutant strain that expressed a much-reduced amount of the dimeric LH1-RC, indicating an important role for protein-U in dimerization of the LH1-RC complex. PufX was located opposite protein-U on the LH1-ring opening, and both its position and conformation differed from that of previous reports of dimeric LH1-RC structures obtained at low-resolution. Twenty-six molecules of the carotenoid spheroidene arranged in two distinct configurations were resolved in the Rba. sphaeroides LH1 and were positioned within the complex to block its pores. Our findings offer a new view of the core photocomplex of Rba. sphaeroides and the connections between structure and function in bacterial photocomplexes in general.

biochemistry↗

bioRxiv2021

Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum

We present a cryo-EM structure of the light-harvesting-reaction center (LH1-RC) core complex from purple phototrophic bacterium Rhodospirillum (Rsp.) rubrum at 2.76 [A] resolution. The LH1 complex forms a closed, slightly elliptical ring structure with 16 {beta}-polypeptides surrounding the RC. Our biochemical analysis detected rhodoquinone (RQ) molecules in the purified LH1-RC, and the cryo-EM density map specifically positions RQ at the QA site in the RC. The geranylgeraniol sidechains of bacteriochlorophyll (BChl) aG coordinated by LH1 {beta}-polypeptides exhibit a highly homologous tail-up conformation that allows for interactions with the bacteriochlorin rings of nearby LH1 -associated BChls aG. The structure also revealed key protein-protein interactions in both N- and C-terminal regions of the LH1 {beta}-polypeptides, mainly within a face-to-face structural subunit. Our findings enable to evaluate past experimental and computational results obtained with this widely used organism and provide crucial information for more detailed exploration of light-energy conversion, quinone transport, and structure-function relationships in pigment-protein complexes.

biochemistry↗

bioRxiv2018

ReALLEN: structural variation discovery in cancer genome by sensitive analysis of single-end reads.

BackgroundThe structural abnormalities in chromosomes are important issues in cancer genomics. Next generation sequencing technologies have big potentials to detect the structural variations precisely and comprehensively. Nevertheless, it is still difficult problem to detect large structural variations from short read sequence data. Major efforts have been achieved with paired-end reads, since discordant pairs directly reflect the existence of large rearrangement. Furthermore, approaches to detect structural variations from single-end reads are still worthwhile challenge because they allow wide choices of sequencing platforms.\n\nResultWe present ReALLEN, a series of tools to detect genomic rearrangement with base-pair resolution from single-end reads provided by next generation sequencing. We examined the performance of ReALLEN using simulated dataset and real dataset sequenced by Ion Torrent systems. In most cases on the simulated dataset, ReALLEN showed nearly 100% precision and better sensitivity than other major tools. Notably, ReALLEN showed stable scores even if it was on some unfavorable conditions, for example, low coverage or small variant size. On the real dataset sequenced by Ion Torrent systems, ReALLEN accurately found an insertional translocation that was crucial for the diagnosis of chronic myeloid leukemia.\n\nConclusionReALLEN is useful to researchers in finding genomic rearrangements. It will contribute to discovery of cancer-specific fusion proteins, precise diagnosis of known types of cancers, and understanding of genetic diseases caused by abnormal chromosomes.

bioinformatics↗