Complete genome sequence of Allochromatium vinosum DSM 180T

Weißgerber, Thomas; Zigann, Renate; Bruce, David; Chang, Yen‐Hsiang; Detter, John C.; Han, Cliff; Hauser, Loren; Jeffries, Cynthia D.; Land, Miriam; Munk, A. Christine; Tapia, Roxanne; Dahl, Christiane

doi:10.4056/sigs.2335270

Cited by 69 publications

(57 citation statements)

References 111 publications

(110 reference statements)

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“…vinosum is a motile, anoxygenic purple sulfur bacterium that lives in sulfide-rich water and sediments (47). M. marinus is a motile, obligately microaerophilic, magnetotactic bacterium that also relies on sulfide or thiosulfate oxidation (48).…”

Section: Resultsmentioning

confidence: 99%

Optogenetic Module for Dichromatic Control of c-di-GMP Signaling

et al. 2017

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Many aspects of bacterial physiology and behavior, including motility, surface attachment, and the cell cycle, are controlled by cyclic di-GMP (c-di-GMP)-dependent signaling pathways on the scale of seconds to minutes. Interrogation of such processes in real time requires tools for introducing rapid and reversible changes in intracellular c-di-GMP levels. Inducing the expression of genes encoding c-di-GMP-synthetic (diguanylate cyclases) and -degrading (c-di-GMP phosphodiesterase) enzymes by chemicals may not provide adequate temporal control. In contrast, light-controlled diguanylate cyclases and phosphodiesterases can be quickly activated and inactivated. A red/near-infrared-light-regulated diguanylate cyclase, BphS, was engineered previously, yet a complementary light-activated c-di-GMP phosphodiesterase has been lacking. In search of such a phosphodiesterase, we investigated two homologous proteins from Allochromatium vinosum and Magnetococcus marinus, designated BldP, which contain C-terminal EAL-BLUF modules, where EAL is a c-di-GMP phosphodiesterase domain and BLUF is a blue light sensory domain. Characterization of the BldP proteins in Escherichia coli and in vitro showed that they possess light-activated c-di-GMP phosphodiesterase activities. Interestingly, light activation in both enzymes was dependent on oxygen levels. The truncated EAL-BLUF fragment from A. vinosum BldP lacked phosphodiesterase activity, whereas a similar fragment from M. marinus BldP, designated EB1, possessed such activity that was highly (Ͼ30-fold) upregulated by light. Following light withdrawal, EB1 reverted to the inactive ground state with a half-life of ϳ6 min. Therefore, the bluelight-activated phosphodiesterase EB1 can be used in combination with the red/nearinfrared-light-regulated diguanylate cyclase BphS for the bidirectional regulation of c-di-GMP-dependent processes in E. coli as well as other bacterial and nonbacterial cells.IMPORTANCE Regulation of motility, attachment to surfaces, the cell cycle, and other bacterial processes controlled by the c-di-GMP signaling pathways occur at a fast (seconds-to-minutes) pace. Interrogation of these processes at high temporal and spatial resolution using chemicals is difficult or impossible, while optogenetic approaches may prove useful. We identified and characterized a robust, blue-lightactivated c-di-GMP phosphodiesterase (hydrolase) that complements a previously engineered red/near-infrared-light-regulated diguanylate cyclase (c-di-GMP synthase). These two enzymes form a dichromatic module for manipulating intracellular c-di-GMP levels in bacterial and nonbacterial cells.KEYWORDS biofilms, c-di-GMP, diguanylate cyclase, gene expression, motility, optogenetics, phosphodiesterase, photoreceptors, photosensory reception, signal transduction S ignaling via second messengers occurs at various time scales, from seconds to hours. To control relatively slow processes, intracellular concentrations of a second messenger can be modulated by the constitutive or inducible (over)e...

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Section: Resultsmentioning

confidence: 99%

Optogenetic Module for Dichromatic Control of c-di-GMP Signaling

et al. 2017

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“…For the oxidation of sulfide, A. vinosum possesses the genetic equipment for at least three different enzymes catalysing this reaction, namely the soluble periplasmic flavocytochrome c and the membrane-bound sulfide : quinone oxidoreductases SqrD and SqrF. The last two are both predicted to be oriented towards the periplasm (Reinartz et al, 1998;Gregersen et al, 2011;Weissgerber et al, 2011). In A. vinosum, the sulfur globules are deposited in the same cellular compartment as the periplasmic thiosulfateand sulfide-oxidizing enzymes.…”

Section: Introductionmentioning

confidence: 99%

“…The substrates of purple sulfur bacteria primarily include sulfide and elemental sulfur (Imhoff, 2005a). A. vinosum is a metabolically especially versatile purple sulfur bacterium that can also utilize thiosulfate and sulfite (Imhoff et al, 1998;Weissgerber et al, 2011). The first major process in the oxidation of thiosulfate and sulfide is the formation of intracellularly stored sulfur globules.…”

Section: Introductionmentioning

confidence: 99%

Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: identification of SoeABC as a major player and relevance of SoxYZ in the process

et al. 2013

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In phototrophic sulfur bacteria, sulfite is a well-established intermediate during reduced sulfur compound oxidation. Sulfite is generated in the cytoplasm by the reverse-acting dissimilatory sulfite reductase DsrAB. Many purple sulfur bacteria can even use externally available sulfite as a photosynthetic electron donor. Nevertheless, the exact mode of sulfite oxidation in these organisms is a long-standing enigma. Indirect oxidation in the cytoplasm via adenosine-59-phosphosulfate (APS) catalysed by APS reductase and ATP sulfurylase is neither generally present nor essential. The inhibition of sulfite oxidation by tungstate in the model organism Allochromatium vinosum indicated the involvement of a molybdoenzyme, but homologues of the periplasmic molybdopterin-containing SorAB or SorT sulfite dehydrogenases are not encoded in genome-sequenced purple or green sulfur bacteria. However, genes for a membrane-bound polysulfide reductase-like iron-sulfur molybdoprotein (SoeABC) are universally present. The catalytic subunit of the protein is predicted to be oriented towards the cytoplasm. We compared the sulfide-and sulfite-oxidizing capabilities of A. vinosum WT with single mutants deficient in SoeABC or APS reductase and the respective double mutant, and were thus able to prove that SoeABC is the major sulfite-oxidizing enzyme in A. vinosum and probably also in other phototrophic sulfur bacteria. The genes also occur in a large number of chemotrophs, indicating a general importance of SoeABC for sulfite oxidation in the cytoplasm. Furthermore, we showed that the periplasmic sulfur substrate-binding protein SoxYZ is needed in parallel to the cytoplasmic enzymes for effective sulfite oxidation in A. vinosum and provided a model for the interplay between these systems despite their localization in different cellular compartments.

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“…A. vinosum has been adopted as a model organism for laboratory-based studies of oxidative sulfur metabolism. Cultivation is comparatively easy, the organism is genetically accessible (4,5), the complete genomic sequence is available (6), and a system for complementation of mutations exists (7)(8)(9).…”

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“…Thiosulfate is fed into the Dsr pathway by the periplasmic Sox proteins (SoxXAK, SoxYZ, SoxB, and SoxL) (2,6,9,12,13). The periplasmic sulfur globules that are formed as the products of these oxidative processes are enclosed by a monolayered hydrophobic protein envelope.…”

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A Comparative Quantitative Proteomic Study Identifies New Proteins Relevant for Sulfur Oxidation in the Purple Sulfur Bacterium Allochromatium vinosum

Weißgerber

Sylvester

Kröninger

et al. 2014

Appl Environ Microbiol

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bIn the present study, we compared the proteome response of Allochromatium vinosum when growing photoautotrophically in the presence of sulfide, thiosulfate, and elemental sulfur with the proteome response when the organism was growing photoheterotrophically on malate. Applying tandem mass tag analysis as well as two-dimensional (2D) PAGE, we detected 1,955 of the 3,302 predicted proteins by identification of at least two peptides (59.2%) and quantified 1,848 of the identified proteins. Altered relative protein amounts (>1.5-fold) were observed for 385 proteins, corresponding to 20.8% of the quantified A. vinosum proteome. A significant number of the proteins exhibiting strongly enhanced relative protein levels in the presence of reduced sulfur compounds are well documented essential players during oxidative sulfur metabolism, e.g., the dissimilatory sulfite reductase DsrAB. Changes in protein levels generally matched those observed for the respective relative mRNA levels in a previous study and allowed identification of new genes/proteins participating in oxidative sulfur metabolism. One gene cluster (hyd; Alvin_2036-Alvin_2040) and one hypothetical protein (Alvin_2107) exhibiting strong responses on both the transcriptome and proteome levels were chosen for gene inactivation and phenotypic analyses of the respective mutant strains, which verified the importance of the so-called Isp hydrogenase supercomplex for efficient oxidation of sulfide and a crucial role of Alvin_2107 for the oxidation of sulfur stored in sulfur globules to sulfite. In addition, we analyzed the sulfur globule proteome and identified a new sulfur globule protein (SgpD; Alvin_2515).

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Complete genome sequence of Allochromatium vinosum DSM 180T

Cited by 69 publications

References 111 publications

Optogenetic Module for Dichromatic Control of c-di-GMP Signaling

Optogenetic Module for Dichromatic Control of c-di-GMP Signaling

Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: identification of SoeABC as a major player and relevance of SoxYZ in the process

A Comparative Quantitative Proteomic Study Identifies New Proteins Relevant for Sulfur Oxidation in the Purple Sulfur Bacterium Allochromatium vinosum

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