dRNA-seq implicates sulfide as master regulator of S(0) metabolism in Chlorobaculum tepidum and other green sulfur bacteria

AbstractThe green sulfur bacteria (Chlorobiaceae) are anaerobes that use electrons from reduced sulfur compounds (sulfide, S(0), and thiosulfate) as electron donors for photoautotrophic growth. Chlorobaculum tepidum, the model system for the Chlorobiaceae, both produces and consumes extracellular S(0) globules depending on the availability of sulfide in the environment. These physiological changes imply significant changes in gene regulation, which has been observed when sulfide is added to Cba. tepidum growing on thiosulfate. However, the underlying mechanisms driving these gene expression changes, i.e. specific regulators and promoter elements involved, have not yet been defined. Here, differential RNA-seq (dRNA-seq) was used to globally identify transcript start sites (TSS) that were present during growth on sulfide, biogenic S(0), and thiosulfate as sole electron donors. TSS positions were used in combination with RNA-seq data from cultures growing on these same electron donors to identify both basal promoter elements and motifs associated with electron donor dependent transcriptional regulation. These motifs were conserved across homologous Chlorobiaceae promoters. Two lines of evidence suggest that sulfide mediated repression is the dominant regulatory mode in Cba. tepidum. First, motifs associated with genes regulated by sulfide overlap key basal promoter elements. Second, deletion of the gene CT1277, encoding a putative regulatory protein, leads to constitutive over-expression of the sulfide:quinone oxidoreductase CT1087 in the absence of sulfide. The results suggest that sulfide is the master regulator of sulfur metabolism in Cba. tepidum and the Chlorobiaceae. Finally, the identification of basal promoter elements with differing strengths will further the development of synthetic biology in Cba. tepidum and perhaps other Chlorobiaceae.ImportanceElemental sulfur is a key intermediate in biogeochemical sulfur cycling. The photoautotrophic green sulfur bacterium Chlorobaculum tepidum both produces and consumes elemental sulfur depending on the availability of sulfide in the environment. Our results reveal transcriptional dynamics of Chlorobaculum tepidum on elemental sulfur, and increase our understanding of the mechanisms of transcriptional regulation governing growth on different reduced sulfur compounds. This study identifies new genes and sequence motifs that likely play significant roles in the production and consumption of elemental sulfur. Beyond this focused impact, this study paves the way for the development of synthetic biology in Chlorobaculum tepidum and other Chlorobiaceae by providing a comprehensive identification of promoter elements to control gene expression, a key element of strain engineering.

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Differential RNA Sequencing Implicates Sulfide as the Master Regulator of S 0 Metabolism in Chlorobaculum tepidum and Other Green Sulfur Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.01966-17 ◽

2017 ◽

Vol 84 (3) ◽

Cited By ~ 1

Author(s):

Jacob M. Hilzinger ◽

Vidhyavathi Raman ◽

Kevin E. Shuman ◽

Brian J. Eddie ◽

Thomas E. Hanson

Keyword(s):

Gene Expression ◽

Elemental Sulfur ◽

Green Sulfur Bacteria ◽

Electron Donors ◽

Reduced Sulfur Compounds ◽

Promoter Elements ◽

Content Type ◽

Sulfur Bacteria ◽

Chlorobaculum Tepidum ◽

Green Sulfur

ABSTRACT The green sulfur bacteria ( Chlorobiaceae ) are anaerobes that use electrons from reduced sulfur compounds (sulfide, S 0 , and thiosulfate) as electron donors for photoautotrophic growth. Chlorobaculum tepidum , the model system for the Chlorobiaceae , both produces and consumes extracellular S 0 globules depending on the availability of sulfide in the environment. These physiological changes imply significant changes in gene regulation, which has been observed when sulfide is added to Cba. tepidum growing on thiosulfate. However, the underlying mechanisms driving these gene expression changes, i.e., the specific regulators and promoter elements involved, have not yet been defined. Here, differential RNA sequencing (dRNA-seq) was used to globally identify transcript start sites (TSS) that were present during growth on sulfide, biogenic S 0 , and thiosulfate as sole electron donors. TSS positions were used in combination with RNA-seq data from cultures growing on these same electron donors to identify both basal promoter elements and motifs associated with electron donor-dependent transcriptional regulation. These motifs were conserved across homologous Chlorobiaceae promoters. Two lines of evidence suggest that sulfide-mediated repression is the dominant regulatory mode in Cba. tepidum . First, motifs associated with genes regulated by sulfide overlap key basal promoter elements. Second, deletion of the Cba. tepidum 1277 ( CT1277 ) gene, encoding a putative regulatory protein, leads to constitutive overexpression of the sulfide:quinone oxidoreductase CT1087 in the absence of sulfide. The results suggest that sulfide is the master regulator of sulfur metabolism in Cba. tepidum and the Chlorobiaceae . Finally, the identification of basal promoter elements with differing strengths will further the development of synthetic biology in Cba. tepidum and perhaps other Chlorobiaceae . IMPORTANCE Elemental sulfur is a key intermediate in biogeochemical sulfur cycling. The photoautotrophic green sulfur bacterium Chlorobaculum tepidum either produces or consumes elemental sulfur depending on the availability of sulfide in the environment. Our results reveal transcriptional dynamics of Chlorobaculum tepidum on elemental sulfur and increase our understanding of the mechanisms of transcriptional regulation governing growth on different reduced sulfur compounds. This report identifies genes and sequence motifs that likely play significant roles in the production and consumption of elemental sulfur. Beyond this focused impact, this report paves the way for the development of synthetic biology in Chlorobaculum tepidum and other Chlorobiaceae by providing a comprehensive identification of promoter elements for control of gene expression, a key element of strain engineering.

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“Candidatus Chlorobium masyuteum,” a Novel Photoferrotrophic Green Sulfur Bacterium Enriched From a Ferruginous Meromictic Lake

Frontiers in Microbiology ◽

10.3389/fmicb.2021.695260 ◽

2021 ◽

Vol 12 ◽

Author(s):

Nicholas Lambrecht ◽

Zackry Stevenson ◽

Cody S. Sheik ◽

Matthew A. Pronschinske ◽

Hui Tong ◽

...

Keyword(s):

Genetic Basis ◽

Tca Cycle ◽

Green Sulfur Bacteria ◽

Sulfur Compounds ◽

Electron Donors ◽

Anoxygenic Phototrophic Bacteria ◽

Reduced Sulfur Compounds ◽

Sulfur Bacteria ◽

Green Sulfur ◽

Reduced Sulfur

Anoxygenic phototrophic bacteria can be important primary producers in some meromictic lakes. Green sulfur bacteria (GSB) have been detected in ferruginous lakes, with some evidence that they are photosynthesizing using Fe(II) as an electron donor (i.e., photoferrotrophy). However, some photoferrotrophic GSB can also utilize reduced sulfur compounds, complicating the interpretation of Fe-dependent photosynthetic primary productivity. An enrichment (BLA1) from meromictic ferruginous Brownie Lake, Minnesota, United States, contains an Fe(II)-oxidizing GSB and a metabolically flexible putative Fe(III)-reducing anaerobe. “Candidatus Chlorobium masyuteum” grows photoautotrophically with Fe(II) and possesses the putative Fe(II) oxidase-encoding cyc2 gene also known from oxygen-dependent Fe(II)-oxidizing bacteria. It lacks genes for oxidation of reduced sulfur compounds. Its genome encodes for hydrogenases and a reverse TCA cycle that may allow it to utilize H2 and acetate as electron donors, an inference supported by the abundance of this organism when the enrichment was supplied by these substrates and light. The anaerobe “Candidatus Pseudopelobacter ferreus” is in low abundance (∼1%) in BLA1 and is a putative Fe(III)-reducing bacterium from the Geobacterales ord. nov. While “Ca. C. masyuteum” is closely related to the photoferrotrophs C. ferroooxidans strain KoFox and C. phaeoferrooxidans strain KB01, it is unique at the genomic level. The main light-harvesting molecule was identified as bacteriochlorophyll c with accessory carotenoids of the chlorobactene series. BLA1 optimally oxidizes Fe(II) at a pH of 6.8, and the rate of Fe(II) oxidation was 0.63 ± 0.069 mmol day–1, comparable to other photoferrotrophic GSB cultures or enrichments. Investigation of BLA1 expands the genetic basis for phototrophic Fe(II) oxidation by GSB and highlights the role these organisms may play in Fe(II) oxidation and carbon cycling in ferruginous lakes.

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Architecture of the photosynthetic complex from a green sulfur bacterium

Science ◽

10.1126/science.abb6350 ◽

2020 ◽

Vol 370 (6519) ◽

pp. eabb6350

Author(s):

Jing-Hua Chen ◽

Hangjun Wu ◽

Caihuang Xu ◽

Xiao-Chi Liu ◽

Zihui Huang ◽

...

Keyword(s):

Photosynthetic Apparatus ◽

Green Sulfur Bacteria ◽

Type I ◽

Type Ii ◽

Common Features ◽

Sulfur Bacteria ◽

Chlorobaculum Tepidum ◽

Cryo Electron Microscopy ◽

Green Sulfur ◽

Insight Into

The photosynthetic apparatus of green sulfur bacteria (GSB) contains a peripheral antenna chlorosome, light-harvesting Fenna-Matthews-Olson proteins (FMO), and a reaction center (GsbRC). We used cryo–electron microscopy to determine a 2.7-angstrom structure of the FMO-GsbRC supercomplex from Chlorobaculum tepidum. The GsbRC binds considerably fewer (bacterio)chlorophylls [(B)Chls] than other known type I RCs do, and the organization of (B)Chls is similar to that in photosystem II. Two BChl layers in GsbRC are not connected by Chls, as seen in other RCs, but associate with two carotenoid derivatives. Relatively long distances of 22 to 33 angstroms were observed between BChls of FMO and GsbRC, consistent with the inefficient energy transfer between these entities. The structure contains common features of both type I and type II RCs and provides insight into the evolution of photosynthetic RCs.

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ON THE ENERGETICS OF THE PHOTOSYNTHESES IN GREEN SULFUR BACTERIA

The Journal of General Physiology ◽

10.1085/jgp.36.2.161 ◽

1952 ◽

Vol 36 (2) ◽

pp. 161-171 ◽

Cited By ~ 30

Author(s):

Helge Larsen ◽

C. S. Yocum ◽

C. B. van Niel

Keyword(s):

Electron Donor ◽

Green Sulfur Bacteria ◽

Co2 Assimilation ◽

Green Plant ◽

Electron Donors ◽

Sulfur Bacteria ◽

Chlorobium Thiosulfatophilum ◽

Plant Photosynthesis ◽

Green Sulfur ◽

Primary Photochemical Reaction

The quantum efficiency of photosynthesis by the green sulfur bacterium, Chlorobium thiosulfatophilum, has been determined in systems in which thiosulfate, tetrathionate, and molecular hydrogen served as electron donors. It was found that about 10 ± 1 quanta are used for the assimilation of 1 molecule of CO2, and that the quantum number is independent of the nature of the electron donor. These results are considered as support for the view that also in the bacterial photosyntheses the primary photochemical reaction consists in the photolysis of H2O, and that the chemical energy released during the oxidation of the electron donor is not utilized for CO2 assimilation. Hence the photosynthetic processes of the green sulfur bacteria are thermodynamically less efficient than is green plant photosynthesis.

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Gene Expression System in Green Sulfur Bacteria by Conjugative Plasmid Transfer

PLoS ONE ◽

10.1371/journal.pone.0082345 ◽

2013 ◽

Vol 8 (11) ◽

pp. e82345 ◽

Cited By ~ 8

Author(s):

Chihiro Azai ◽

Jiro Harada ◽

Hirozo Oh-oka

Keyword(s):

Gene Expression ◽

Expression System ◽

Green Sulfur Bacteria ◽

Plasmid Transfer ◽

Conjugative Plasmid ◽

Gene Expression System ◽

Conjugative Plasmid Transfer ◽

Sulfur Bacteria ◽

Green Sulfur

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Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom

10.1101/604504 ◽

2019 ◽

Author(s):

Srijak Bhatnagar ◽

Elise S. Cowley ◽

Sebastian H. Kopf ◽

Sherlynette Pérez Castro ◽

Sean Kearney ◽

...

Keyword(s):

Community Dynamics ◽

Microbial Mats ◽

Elemental Sulfur ◽

Green Sulfur Bacteria ◽

Sulfur Cycle ◽

Ecological Niches ◽

Purple Sulfur Bacteria ◽

Microbial Community Dynamics ◽

Sulfur Bacteria ◽

Green Sulfur

AbstractPhototrophic microbial mats commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. Here we show that similar coexistence patterns and ecological niches can occur in suspended phototrophic blooms of an organic-rich estuary. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophicCyanobacteria, the middle and lower parts were dominated by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We found multiple uncultured phototrophic lineages and present metagenome-assembled genomes of two uncultured organisms within theChlorobiales. Apparently, thoseChlorobialespopulations were affected byMicroviridaeviruses. We suggest a sulfur cycle within the bloom in which elemental sulfur produced by phototrophs is reduced to sulfide byDesulfuromonas sp. These findings improve our understanding of the ecology and ecophysiology of phototrophic blooms and their impact on biogeochemical cycles.

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