Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake

Tanaka, Yoshiki; Yoshikaie, Kunihito; Takeuchi, Azusa; Ichikawa, Muneyoshi; Mori, Tomoyuki; Uchino, S.; Sugano, Yasunori; Hakoshima, Toshio; Takagi, Hiroshi; Nonaka, Gen; Tsukazaki, Tomoya

doi:10.1126/sciadv.aba7637

Cited by 31 publications

(68 citation statements)

References 41 publications

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“…Hdr genes in one Ca. Stygibacter MAG (3300025642_13) are within a gene cluster that also contains genes implicated in sulfur metabolism, including thiosulfate:sulfurtransferase (TST) (with a predicted signal peptide), a cytoplasmic sulfur relay protein TusA, and a sulfur compound transporter ( Gristwood et al, 2011 ; Tanaka et al, 2020 ). Homologs of these four proteins are also encoded in MAGs assigned to Ca.…”

Section: Resultsmentioning

confidence: 99%

Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake

et al. 2021

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The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial “dark matter” taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hills), novel lineages and novel metabolic traits were identified for both phyla. The Cloacimonadota MAGs exhibited a capacity for carbon fixation using the reverse tricarboxylic acid cycle driven by oxidation of hydrogen and sulfur. Certain Cloacimonadota MAGs encoded proteins that possess dockerin and cohesin domains, which is consistent with the assembly of extracellular cellulosome-like structures that are used for degradation of polypeptides and polysaccharides. The Omnitrophota MAGs represented phylogenetically diverse taxa that were predicted to possess a strong biosynthetic capacity for amino acids, nucleosides, fatty acids, and essential cofactors. All of the Omnitrophota were inferred to be obligate fermentative heterotrophs that utilize a relatively narrow range of organic compounds, have an incomplete tricarboxylic acid cycle, and possess a single hydrogenase gene important for achieving redox balance in the cell. We reason that both Cloacimonadota and Omnitrophota form metabolic interactions with hydrogen-consuming partners (methanogens and Desulfobacterota, respectively) and, therefore, occupy specific niches in Ace Lake.

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Section: Resultsmentioning

confidence: 99%

Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake

et al. 2021

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“…At SPring-8 beamline BL32XU, we achieved phase determination on in meso crystals of the membrane protein YeeE from a dataset obtained by SWSX using ZOO (Tanaka et al, 2020). Absorbed dose and wedge size for data collection were set to 10 MGy and 7 , respectively, since a definitive guideline for phasing data collection was not clear at the time.…”

Section: Siras Phasing Of Membrane Protein Yeee With Swsxmentioning

confidence: 99%

“…In this structure analysis, selenium (Se) peak wavelength and native datasets from the YeeE in meso crystals were analyzed using SIRAS (single isomorphous replacement with anomalous scattering). Detailed information on crystallization and data collection are summarized by Tanaka et al (2020) and Table 5 therein, respectively. Crystal sizes roughly corresponding to 30 mm and 10 mm (H) Â 15 mm (V) beam, which was the maximum useable at beamline BL32XU, were used for raster scan and data collection.…”

Section: Siras Phasing Of Membrane Protein Yeee With Swsxmentioning

confidence: 99%

Guidelines for de novo phasing using multiple small-wedge data collection

Baba¹,

Matsuura²,

Kawamura³

et al. 2021

J Synchrotron Rad

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Intense micro-focus X-ray beamlines available at synchrotron facilities have achieved high-quality data collection even from the microcrystals of membrane proteins. The automatic data collection system developed at SPring-8, named ZOO, has contributed to many structure determinations of membrane proteins using small-wedge synchrotron crystallography (SWSX) datasets. The `small-wedge' (5–20°) datasets are collected from multiple crystals and then merged to obtain the final structure factors. To our knowledge, no systematic investigation on the dose dependence of data accuracy has so far been reported for SWSX, which is between `serial crystallography' and `rotation crystallography'. Thus, herein, we investigated the optimal dose conditions for experimental phasing with SWSX. Phase determination using anomalous scattering signals was found to be more difficult at higher doses. Furthermore, merging more homogeneous datasets grouped by hierarchical clustering with controlled doses mildly reduced the negative factors in data collection, such as `lack of signal' and `radiation damage'. In turn, as more datasets were merged, more probable phases could be obtained across a wider range of doses. Therefore, our findings show that it is essential to choose a lower dose than 10 MGy for de novo structure determination by SWSX. In particular, data collection using a dose of 5 MGy proved to be optimal in balancing the amount of signal available while reducing the amount of damage as much as possible.

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“…Recently, in Escherichia coli , structural analysis of the membrane protein YeeE, which engages in thiosulfate uptake, was performed (Tanaka et al . 2020 ). However, the detailed mechanism of uptake and utilization of thiosulfate in S. pombe remains obscure.…”

Section: Sulfur Metabolism In S Pombementioning

confidence: 99%

Response to sulfur in Schizosaccharomyces pombe

Ohtsuka

Shimasaki

Aiba

2021

FEMS Yeast Research

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Sulfur is an essential component of various biologically important molecules, including methionine, cysteine, and glutathione, and it is also involved in coping with oxidative and heavy metal stress. Studies using model organisms, including budding yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe), have contributed not only to understanding various cellular processes but also to understanding the utilization and response mechanisms of each nutrient, including sulfur. Although fission yeast can use sulfate as a sulfur source, its sulfur metabolism pathway is slightly different from that of budding yeast because it does not have a trans-sulfuration pathway. In recent years, it has been found that sulfur starvation causes various cellular responses in S. pombe, including sporulation, cell cycle arrest at G2, chronological lifespan extension, autophagy induction, and reduced translation. This MiniReview identifies two sulfate transporters in S. pombe, Sul1 (encoded by SPBC3H7.02) and Sul2 (encoded by SPAC869.05c), and summarizes the metabolic pathways of sulfur assimilation and cellular response to sulfur starvation. Understanding these responses, including metabolism and adaptation, will contribute to a better understanding of the various stress and nutrient starvation responses and chronological lifespan regulation caused by sulfur starvation.

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Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake

Cited by 31 publications

References 41 publications

Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake

Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake

Guidelines for de novo phasing using multiple small-wedge data collection

Response to sulfur in Schizosaccharomyces pombe

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