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Light and polyphosphate kinase 2 cooperatively regulate the production of zero-valent sulfur in a deep-sea bacterium.

ABSTRACT: The existence of light in various deep-sea environments has been well established. Our previous research found blue light promotes zero-valent sulfur (ZVS) production in Erythrobacter flavus 21-3, a bacterium isolated from the deep-sea cold seep. E. flavus 21-3 can convert thiosulfate to ZVS through a novel thiosulfate oxidation pathway comprising a thiosulfate dehydrogenase (TsdA) and two thiosulfohydrolases (SoxB). Using proteomic analysis, bacterial two-hybrid system and heterologous expression assays, we found that infrared light also promotes zero-valent sulfur (ZVS) production in E. flavus 21-3. The bacteriophytochrome (bphp) Ef2bphp-15570 autophosphorylated and activated GGDEF domain-containing protein D0Y83_RS00450 to produce c-di-GMP. Subsequently, the PilZ protein mPilZ-1753 bound to c-di-GMP and activated downstream sulfur oxidation pathways. During this process, polyphosphate kinase 2 (PPK2) affects the content of c-di-GMP by competing for GTP, thereby together c-di-GMP regulating ZVS production, as well as other metabolic processes in E. flavus 21-3. This study provides a novel insight into a deep-sea non-photosynthetic bacterium which sensing infrared light to regulate sulfur metabolism through a bacteriophytochrome photoreceptor, thus offering new understandings perspectives on microbial utilization of light energy.

INSTRUMENT(S):

ORGANISM(S): Erythrobacter

TISSUE(S): Cell Culture

SUBMITTER: zhang tianhang

LAB HEAD: Chaomin Sun

PROVIDER: PXD058843 | Pride | 2025-05-07

REPOSITORIES: Pride

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			Action	DRS
	XA05690DA_Dark_21_3.raw	Raw
	XA05690DA_Dark_ppk.raw	Raw
	XA05690DA_In_21_3.raw	Raw
	XA05690DA_In_ppk.raw	Raw
	checksum.txt	Txt

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Similar Datasets

Blue light promotes zero-valent sulfur production in a deep-sea bacterium

Project description:Bacteria isolated from diverse environments were found to sense blue light to regulate their biological functions. However, this ability of deep-sea bacteria has been studied rarely. In this study, we found serendipitously that blue light stimulated excess zero-valent sulfur (ZVS) production of E. flavus 21-3, which was isolated from the deep-sea cold seep and possessed a novel thiosulfate oxidation pathway. Its ZVS production responding to the blue light was mediated by a light-oxygen-voltage histidine kinase (LOV-1477), a diguanylate cyclase (DGC-2902), a PilZ protein (mPilZ-1753) and the key thiosulfate dehydrogenase (TsdA) in its thiosulfate oxidation pathway. Subsequently, the thiosulfohydrolase (SoxB-277) was found working with another SoxB (SoxB-285) and being as substitute for each other to generate ZVS. This study provided an example of deep-sea bacteria sensing blue light to regulate thiosulfate oxidation. Deep-sea blue light potentially helped these blue-light-sensing bacteria adapt harsh conditions by diversifying their biological processes.

2023-01-03 | PXD035435 | Pride

In situ proteomic data of E. flavus 21-3 and corresponding mutants

Project description:Zero-valent sulfur (ZVS) distributes widely in the deep-sea cold seep, which is important immediate in the active sulfur cycle of cold seep. In our preview work, a novel ZVS formation pathway discovered in the deep-sea cold weep bacterium Erythrobacter flavus 21-3 was described. However, whether this pathway worked and what function roles it played in the cold seep were unknown. In this study, E. flavus 21-3 was verified to produce zero-valent sulfur in the cold seep using genes soxB and tsdA as our preview report described. Based on proteomic data, stoichiometric methods and microscopic observation, this ZVS formation pathway benefited E. flavus 21-3 in the deep-sea cold seep. Notably, 30% metagenomes contained these two genes in the shallow sediments, which present the most abundant sulfur genes and active sulfur cycle in the cold seep sediments. It suggested that this sulfur formation pathway exist across many bacteria in the cold seep. This strongly indicates that this novel pathway might be frequently used by microbes and plays an important role in the biogeochemical sulfur cycle in cold seep.

2022-07-09 | PXD029383 | Pride

Thiosulfate oxidation in Erythrobacter flavus 21-3 provides novel clues to the source of element sulfur in the deep-sea cold seep

Project description:Zero-valent sulfur (ZVS) and thiosulfate are important intermediates in the biogeochemical cycle of sulfur. The former has been proved to be existed in the cold seep and hydrothermal systems. Three thiosulfate oxidation pathways are already identified and here we found a novel one in Erythrobacter, which was the first genus in the family Erythrobacteraceae that could accumulate ZVS during thiosulfate oxidation. Erythrobacter flavus 21-3 was isolated from the sediment of clod seep. Genomic analyses showed the typical genes encoding Sox multienzyme complex were absent in the genome of E. flavus 21-3. Through proteome and genome data, we identified a three gene involved pathway of thiosulfate oxidation, including thiosulfate dehydrogenase (tsdA), thiosulfohydrolase (soxB) and sulfur dioxygenases (sdo). For the first time, genetic operating system was constructed in Erythrobacter, and mutant strains ΔtsdA, ΔsoxB, ΔsdoA, ΔsdoB and ΔsdoAB were constructed. Stoichiometry was calculated and tetrathionate and ZVS were found to be the intermediates in this novel thiosulfate oxidation pathway. The diverse and distribution of these proteins were investigated and this novel thiosulfate oxidation pathway may exist in bacteria formerly ignored the function of ZVS production. The results give a powerful evidence for a new source of biogenetic ZVS in cold seep.

2021-09-09 | PXD016502 | Pride

Generation of zero-valent sulfur from dissimilatory sulfate reduction in sulfate-reducing bacteria

Project description:We report a new DSR pathway that directly generates zero-valent sulfur (ZVS) in phylogenetically diverse SRB.

2023-04-27 | E-MTAB-12239 | biostudies-arrayexpress

Generation of zero-valent sulfur from dissimilatory sulfate reduction in sulfate-reducing microorganisms

Project description:Dissimilatory sulfate reduction (DSR) mediated by sulfate-reducing microorganisms (SRMs) plays a pivotal role in global sulfur, carbon, oxygen, and iron cycles since ~3.5 billion years ago. The canonical DSR pathway is believed to be sulfate reduction to sulfide. Herein, we report a new DSR pathway in phylogenetically diverse SRMs through which zero-valent sulfur (ZVS) is directly generated. We identified that approximately 8.9% of sulfate reduction was directed toward ZVS with S8 as a predominant product, and the ratio of sulfate-to-ZVS could be changed with SRMs’ growth conditions, particularly the medium salinity. Further coculturing experiments and metadata analyses revealed that DSR-derived ZVS supported the growth of various ZVS-metabolizing microorganisms, highlighting this new pathway as an essential component of the sulfur biogeochemical cycle

2023-04-28 | PXD040825 | Pride

Role of thiosulfate as a source of energy in the bathypelagic North Atlantic Ocean

Project description:The available energy and carbon sources for prokaryotes in the deep ocean remain still largely enigmatic. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes. Shipboard experiments performed in the North Atlantic using Labrador Sea Water (~2000 m depth) amended with thiosulfate led to an enhanced prokaryotic dissolved inorganic carbon (DIC) fixation.

2021-04-30 | GSE136729 | GEO

The cyanobacterial phytochrome 2 regulates the expression of motility-related genes through the second messenger cyclic di-GMP

Project description:The cyanobacterial phytochrome Cph2 is a light-dependent diguanylate cyclase producing the second messenger c-di-GMP. Under blue light, the Cph2-dependent increase in the cellular c-di-GMP concentration leads to inhibition of motility in the cyanobacterium Synechocystis 6803. However, the targets of c-di-GMP in this cyanobacterium and its mechanism of action remained unclear. Here, we determined the cellular concentrations of three cyclic nucleotides in wild-type and Δcph2 cells after blue- and green light illumination. Inactivation of the photoreceptor gene completely abolished the blue-light dependent increase in the c-di-GMP content. Microarray analysis revealed that in the wild type in comparison to the Δcph2 mutant, blue light mainly led to a change in accumulation of mRNAs encoding minor pilins, putative chaperone usher pili as well as several chemotaxis regulators. The mRNA encoding the minor pilins pilA5-pilA6 is negatively affected by high c-di GMP content under blue light, whereas the minor pilin encoding operon pilA9-slr2018 accumulates under the same conditions, suggesting opposing functions of the respective gene sets. Based on mutational and gene expression analysis, we further suggest that the second Synechocystis 6803 homolog of a CRP-like transcription factor, SyCRP2, is the regulator of minor pilin gene expression and of putative chaperone usher pili genes slr1667/slr1668. Thus, our work indicates that the Cph2-mediated increase in cellular c-di-GMP concentration upon blue-light illumination specifically changes the transcriptome of Synechocystis 6803.

2020-03-23 | GSE116409 | GEO

Expression data from Aracidopsis roots

Project description:Sulfate is recognized as a primary sulfur source for plant growth and effects of thiosulfate as a sulfur source on plant growth and metabolism, gene expression have not been studied. We used microarrays to detail the global programme of gene expression in response to thiosulfate as a sulfur source.

2019-08-01 | GSE118293 | GEO

Differential proteomics of Desulfurella amilsii to explore sulfur reductive metabolism

Project description:Desulfurella amilsii is an acidotolerant sulfur-reducing bacterium isolated from sediments of an acidic river. It can grow in a broad range of pH and can obtain energy via respiring elemental sulfur or thiosulfate, as well as by disproportionating elemental sulfur. Its genome encodes the enzyme sulfur reductase, and several rhodanese-like proteins, possibly playing a role in sulfur respiration and disproportionation. Thiosulfate reductase and dissimilatory sulfite reductase are encoded and might play a role during the respiration of thiosulfate. The involvement of these enzymes in the reductive routes of sulfur metabolism is not yet clearly understood. Desulfurella amilsii was used in this study to combine strategies for sulfur metabolism research on the protein level to shed some light on the pathways involved in the metabolism of this microorganism.

2018-10-19 | PXD008496 | Pride

The response to thiosulfate availability in Hyphomicrobium denitrificans

Project description:Many sulfur-oxidizing prokaryotes oxidize sulfur compounds through a combination of initial extracytoplasmic and downstream cytoplasmic reactions. Facultative sulfur oxidizers adjust transcription to sulfur availability. While sulfur-oxidizing enzymes and transcriptional repressors have been extensively studied, sulfur import into the cytoplasm and how regulators sense external sulfur are poorly understood. Addressing this gap, we show that SoxT1A and SoxT1B, which resemble YeeE/YedE-family thiosulfate transporters and are encoded alongside sulfur oxidation and transcriptional regulation genes, fulfill these roles in the Alphaproteobacterium Hyphomicrobium denitrificans. RT-qPCR provided initial evidence that SoxT1A and SoxT1B from H. denitrificans may be intricate components of the oxidation pathway and/or involved in its transcriptional regulation. Here, we extend these analyses with genome-wide mRNA-Seq data for the reference strain, comparing transcription in the absence and presence of 2 mM thiosulfate

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