Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillusspecies

Rey, Michael W.; Ramaiya, Preethi; Nelson, Beth A.; Brody-Karpin, Shari D; Zaretsky, Elizabeth J; Tang, Maria; Leon, Alfredo Lopez de; Xiang, Henry; Gusti, Veronica; Clausen, Ib Groth; Olsen, Peter Bjarke; Rasmussen, Michael; Andersen, Jens T.; Jørgensen, P. E. V.; Larsen, T. S.; Sorokin, Alexeï; Bolotin, Alexander; Lapidus, Alla; Galleron, Nathalie; Ehrlich, S. Dusko; Berka, Randy M.

doi:10.1186/gb-2004-5-10-r77

Cited by 326 publications

(145 citation statements)

References 55 publications

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“…In contrast, the YkuV protein we cloned could easily be expressed in E. coli. In addition, the new protein sequence containing this difference is locally well aligned with its homolog, the YkuV protein from Bacillus licheniformis, which is considered the closest relative species of B. subtilis (51). Furthermore, the secondary structure prediction in combination with the homology modeling indicated that the altered residues do not change the secondary structures, and the extended residues have no effect on the global fold.…”

Section: Resultsmentioning

confidence: 97%

The Bacillus subtilis YkuV Is a Thiol:Disulfide Oxidoreductase Revealed by Its Redox Structures and Activity

Zhang

Hu²,

Guo³

et al. 2006

Journal of Biological Chemistry

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The Bacillus subtilis YkuV responds to environmental oxidative stress and plays an important role for the bacteria to adapt to the environment. Bioinformatic analysis suggests that YkuV is a homolog of membrane-anchored proteins and belongs to the thioredoxin-like protein superfamily containing the typical Cys-Xaa-XaaCys active motif. However, the biological function of this protein remains unknown thus far. In order to elucidate the biological function, we have determined the solution structures of both the oxidized and reduced forms of B. subtilis YkuV by NMR spectroscopy and performed biochemical studies. Our results demonstrated that the reduced YkuV has a low midpoint redox potential, allowing it to reduce a variety of protein substrates. The overall structures of both oxidized and reduced forms are similar, with a typical thioredoxinlike fold. However, significant conformational changes in the CysXaa-Xaa-Cys active motif of the tertiary structures are observed between the two forms. In addition, the backbone dynamics provide further insights in understanding the strong redox potential of the reduced YkuV. Furthermore, we demonstrated that YkuV is able to reduce different protein substrates in vitro. Together, our results clearly established that YkuV may function as a general thiol:disulfide oxidoreductase, which acts as an alternative for thioredoxin or thioredoxin reductase to maintain the reducing environment in the cell cytoplasm.Thioredoxins are small proteins (ϳ12 kDa) that are ubiquitously present in all kinds of life forms from archaebacteria to human (1). Generally, they function as protein thiol:disulfide oxidoreductases for maintaining the reducing environment in cytoplasm, protecting cells against hydrogen peroxide (2) and oxidative stress (3). In addition to the general function as a thiol:disulfide oxidoreductase, some thioredoxins from different organisms are also involved in various specified biological processes and therefore have specific biological functions. For example, thioredoxin is an essential subunit of bacteriophage T7 DNA polymerase in Escherichia coli (4), and in eukaryotes, thioredoxins facilitate the refolding of disulfide-containing proteins (5) and modulate the activity of certain transcription factors (6, 7). Moreover, thioredoxins have been considered as a possible target for drug development because of their roles in stimulating cancer cell growth and as an inhibitor of apoptosis (8).The thioredoxin fold was first characterized from E. coli thioredoxin, which consists of a central five-stranded mixed ␤-sheet surrounded by four ␣-helices (9 -11). Subsequently, the structures of several thioredoxins from different species were determined (11-16). Notably, from E. coli to human, thioredoxins all share the same thioredoxin fold with the Cys-Gly-Pro-Cys active motif. In addition to thioredoxins, a large number of proteins comprising the basic thioredoxin fold with the CysXaa-Xaa-Cys active motif in the active site have been characterized as thioredoxin-like proteins, which co...

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Section: Resultsmentioning

confidence: 97%

The Bacillus subtilis YkuV Is a Thiol:Disulfide Oxidoreductase Revealed by Its Redox Structures and Activity

Zhang

Hu²,

Guo³

et al. 2006

Journal of Biological Chemistry

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“…MC-1) showed no channel activity in previous studies (7). Of the bacteria containing the remaining 26 homologues, six of them were commercially available: B. licheniformis, isolated from soil and plant material (27), and L. vestfoldensis (28), R. sphaeroides (29), S. putrefaciens (30), R. denitrificans (31), and Oceanicaulis sp. (32) isolated from sea water (28 -33).…”

Section: Resultsmentioning

confidence: 99%

Comparative Study of the Gating Motif and C-type Inactivation in Prokaryotic Voltage-gated Sodium Channels

Irie

Kitagawa

Nagura

et al. 2010

Journal of Biological Chemistry

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Prokaryotic voltage-gated sodium channels (Na V s) are homotetramers and are thought to inactivate through a single mechanism, named C-type inactivation. Here we report the voltage dependence and inactivation rate of the NaChBac channel from Bacillus halodurans, the first identified prokaryotic Na V , as well as of three new homologues cloned from Bacillus licheniformis (Na V BacL), Shewanella putrefaciens (Na V SheP), and Roseobacter denitrificans (Na V RosD). We found that, although activated by a lower membrane potential, Na V BacL inactivates as slowly as NaChBac. Na V SheP and Na V RosD inactivate faster than NaChBac. Mutational analysis of helix S6 showed that residues corresponding to the "glycine hinge" and "PXP motif" in voltage-gated potassium channels are not obligatory for channel gating in these prokaryotic Na V s, but mutations in the regions changed the inactivation rates. Mutation of the region corresponding to the glycine hinge in Na V BacL (A214G), Na V SheP (A216G), and NaChBac (G219A) accelerated inactivation in these channels, whereas mutation of glycine to alanine in the lower part of helix S6 in NaChBac (G229A), Na V BacL (G224A), and Na V RosD (G217A) reduced the inactivation rate. These results imply that activation gating in prokaryotic Na V s does not require gating motifs and that the residues of helix S6 affect C-type inactivation rates in these channels.Voltage-gated sodium channels (Na V s) 3 generate the rapid upstroke of action potentials in nerve cell axons (1). In mammalian Na V s, the channel is formed by the ␣-subunit, which comprises four repeats of six-transmembrane segments, with each repeat consisting of 300 -400 amino acids. The ␣-subunit carries several glycosylation sites and co-assembles with auxiliary subunits to form the native channel (2, 3). The only structural information on Na V s available to date is a density map of the Na V from the electric organ of the electric eel determined by cryoelectron microscopy (4). Due to its limited resolution of 19 Å, the density map did not provide insights into the gating or sodium selectivity.The first prokaryotic Na V , NaChBac, was cloned from Bacillus halodurans (5). Subsequently, three more prokaryotic sodium channels were cloned and characterized (6, 7). All studied prokaryotic Na V s form homotetramers with a structure thought to be similar to that of some potassium channels with known structures (8 -10). Furthermore, because the proteins could be expressed in large amounts in Escherichia coli and purified by metal chelate affinity chromatography (5, 7, 11), they are promising candidates for high resolution structure determination and structure-function analyses.The physiological role of prokaryotic Na V s may be related to pH homeostasis, motility, and chemotaxis (6, 12). Searching bacterial genomic data bases, we found 26 sequences of putative NaChBac homologues from bacteria living in various environments. We were able to clone the putative Na V genes from three of these bacteria, Bacillus licheniformis, Shewanella pu...

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“…Bacillus licheniformis is a Gram-positive, spore-forming soil bacterium that is used for the production of enzymes, antibiotics, biochemicals and consumer products on an industrial scale (Li, Yang, & Mu, 2010;Rey et al, 2004;Xie, Guan, & He, 2012). Previously, sequence homology-based studies revealed the identity of proteins involved in the production of antibiotics, leading to the detection of two mesarcidin-like peptide lichecidins in the cell-free culture supernatant of B. licheniformis (ATCC 14580 and DSM 13, respectively).…”

Section: Introductionmentioning

confidence: 99%

Purification and characterization of macrolactins and amicoumacins from Bacillus licheniformis BFP011: a new source of food antimicrobial substances

Arbsuwan

Payoungkiattikun

Sirithorn

et al. 2017

CyTA - Journal of Food

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In this study, Bacillus licheniformis BFP011 has been cultivated for producing antimicrobial compounds, which were concentrated from the crude supernatant and purified using thin-layer chromatography. The antimicrobial activity was investigated in the presence of several organic solvents and detergents, and inhibiting effects to various Gram-negative and Gram-positive human pathogenic and food spoilage bacteria were observed. Three bands (F4, F5 and F6) showing antimicrobial activity against Salmonella typhi ATCC 5784 were subjected to reversed-phase high-performance liquid chromatography purification. Two peaks of fraction F5, F5-P3 and F5-P4, showed 100% inhibition against S. typhi ATCC 5784. The contained mixture of antimicrobial compounds consists of macrolactins and amicoumacins, which induced the collapse and breaking of S. typhi ATCC 5784 cell membranes in a time-dependent manner. Taken collectively, the results indicate that these compounds may represent promising candidates for the development of food preservative agents of natural origin, as well as novel antimicrobial drug candidates against multiresistant bacterial strains.Purificación y caracterización de macrolactinas y amicoumacinas procedentes de Bacillus licheniformis BFP011: una nueva fuente de sustancias antimicrobianas para los alimentos RESUMEN En el presente estudio, se cultivó Bacillus licheniformis BFP011 para producir compuestos antimicrobianos; estos fueron concentrados del sobrenadante crudo y purificado empleando cromatografía en capa fina (CCF). En presencia de varios solventes y detergentes orgánicos se analizó la actividad antimicrobiana, observándose, además, los efectos inhibidores de varias bacterias gram-negativas y gram-positivas, patógenas para los seres humanos y causantes del deterioro de los alimentos. Mediante RP-HPLC se purificaron tres franjas (F4, F5 y F6) que mostraron actividad antimicrobiana contra la Salmonella typhi ATCC 5784, comprobándose que los dos picos de la fracción F5 (F5-P3 y F5-P4) provocan una inhibición del 100% contra la S. typhi ATCC 5784. La mezcla de compuestos antimicrobianos contiene macrolactinas y amicoumacinas; estas produjeron el colapso y el rompimiento de las membranas celulares de S. typhi ATCC 5784 a medida que fue transcurriendo el tiempo. Considerados en su conjunto, estos resultados indican que es posible que dichos compuestos sean sustancias prometedoras para la creación de agentes conservantes de alimentos de origen natural, y para el desarrollo de medicamentos antimicrobianas novedosas contra cepas bacterianas multirresistentes. ARTICLE HISTORY

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Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillusspecies

Cited by 326 publications

References 55 publications

The Bacillus subtilis YkuV Is a Thiol:Disulfide Oxidoreductase Revealed by Its Redox Structures and Activity

The Bacillus subtilis YkuV Is a Thiol:Disulfide Oxidoreductase Revealed by Its Redox Structures and Activity

Comparative Study of the Gating Motif and C-type Inactivation in Prokaryotic Voltage-gated Sodium Channels

Purification and characterization of macrolactins and amicoumacins from Bacillus licheniformis BFP011: a new source of food antimicrobial substances

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