Whole-Genome Sequences of Bacillus subtilis and Close Relatives

Earl, Ashlee M.; Eppinger, Mark; Fricke, W. Florian; Rosovitz, M. J.; Rasko, David A.; Daugherty, S. J.; Losick, Richard; Kolter, Roberto; Ravel, Jacques

doi:10.1128/jb.05675-11

Cited by 56 publications

(42 citation statements)

References 18 publications

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“…The most comprehensive comparative analysis, which now includes nearly 100 strains in the genus Salinispora, argues that species-specific GIs carrying BGCs possess an unspecified functional or adaptive role in the marine environment (18,19). Similar studies in Bacillus argue for the role of GIs in niche adaptation (20). Our study provides an explicit example of adaptation through HGT in which the BGCs for 1 and 4 have been integrated into the chromosome of ant-associated Pseudonocardia spp., whereas 2-3 are encoded by two plasmid-borne BGCs.…”

Section: Discussionmentioning

confidence: 52%

Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants

Sit

Ruzzini

Arnam

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Small molecules produced by Actinobacteria have played a prominent role in both drug discovery and organic chemistry. As part of a larger study of the actinobacterial symbionts of fungus-growing ants, we discovered a small family of three previously unreported piperazic acid-containing cyclic depsipeptides, gerumycins A–C. The gerumycins are slightly smaller versions of dentigerumycin, a cyclic depsipeptide that selectively inhibits a common fungal pathogen, Escovopsis. We had previously identified this molecule from a Pseudonocardia associated with Apterostigma dentigerum, and now we report the molecule from an associate of the more highly derived ant Trachymyrmex cornetzi. The three previously unidentified compounds, gerumycins A–C, have essentially identical structures and were produced by two different symbiotic Pseudonocardia spp. from ants in the genus Apterostigma found in both Panama and Costa Rica. To understand the similarities and differences in the biosynthetic pathways that produced these closely related molecules, the genomes of the three producing Pseudonocardia were sequenced and the biosynthetic gene clusters identified. This analysis revealed that dramatically different biosynthetic architectures, including genomic islands, a plasmid, and the use of spatially separated genetic loci, can lead to molecules with virtually identical core structures. A plausible evolutionary model that unifies these disparate architectures is presented.

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Section: Discussionmentioning

confidence: 52%

Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants

Sit

Ruzzini

Arnam

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…Irigul-Sonmez et al, 2014), but it becomes capable of positively and negatively, albeit mostly in a modest manner, regulating expression of numerous genes involved in a wide range of cellular processes (IrigulSonmez et al, 2014). To ascertain whether the full-length LutR can directly regulate lutP expression and to identify the consensus binding sequence for the full-length LutR, we used the undomesticated B. subtilis strain RO-NN-1, whose genomic sequence is now available (Earl et al, 2012), in the following studies.…”

Section: Resultsmentioning

confidence: 99%

“…The lutR genes from various B. subtilis strains, including NCIB 3610 (GenBank accession number KJ580506), RO-NN-1 (Earl et al, 2012), BAB-1 (GenBank accession number YP_007664070), BEST195 (Nishito et al, 2010), BSn5 (Deng et al, 2011), MB73/2 (GenBank accession number EME08645), W23 (Zeigler, 2011) and XF-1 (Guo et al, 2013), encode a transcriptional regulator of 240 aa belonging to the GntR family [National Center for Biotechnology Information (NCBI) annotation]. The regulators of the GntR family contain a DNA-binding domain at the N terminus of the protein and an effector-binding domain at at the N terminus (NCBI annotation).…”

Section: Resultsmentioning

confidence: 99%

Transcriptional regulation of the l-lactate permease gene lutP by the LutR repressor of Bacillus subtilis RO-NN-1

Chiu¹,

Lin²,

Shaw³

2014

Microbiology

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The Bacillus subtilis lutABC operon encodes three iron-sulfur-containing proteins required for Llactate utilization and involved in biofilm formation. The transcriptional regulator LutR of the GntR family negatively controls lutABC expression. The lutP gene, which is situated immediately upstream of lutR, encodes an L-lactate permease. Here, we show that lutP expression can be strongly induced by L-lactate and is subject to partial catabolite repression by glucose. Disruption of the lutR gene led to a strong derepression of lutP and no further induction by L-lactate, suggesting that the LutR repressor can also negatively control lutP expression. Electrophoretic mobility shift assay revealed a LutR-binding site located downstream of the promoter of lutA or lutP and containing a consensus inverted repeat sequence 59-TCATC-N 1 -GATGA-39. Reporter gene analysis showed that deletion of each LutR-binding site caused a strong derepression of lutA or lutP. These results indicated that these two LutR-binding sites can function as operators in vivo. Moreover, deletion analysis identified a DNA segment upstream of the lutP promoter to be important for lutP expression. In contrast to the truncated LutR of laboratory strains 168 and PY79, the full-length LutR of the undomesticated strain RO-NN-1, and probably many other B. subtilis strains, can directly and negatively regulate lutP transcription. The absence or presence of the N-terminal 21 aa of the full-length LutR, which encompass a small part of the predicted winged helix-turn-helix DNA-binding motif, may probably alter the DNA-binding specificity or affinity of LutR.

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“…Hungate medium [7], used for enrichment, serial dilution and subsequent cultivation of bacteria from ruminal fluid, contained (per 1000 ml) K 2 HPO 4 0.5 g, KH 2 PO 4 0.2 g, (NH 4 ) 2 SO 4 0.5 g, NaCl 1.0 g, MgSO 4 0.02 g, CaCl 2 0.05 g, NaHCO 3 5.0 g, cysteine hydrochloride 0.5 g, starch 5.0 g, clarified rumen fluid 1% and agar 3% at pH 7.2. The medium was pre gassed with N 2 :H 2 (80:20); sterilized at 10 psi followed by post gassing with N 2 :CO 2 (80:20) and sealed with butyl rubber and aluminium seals.…”

Section: Media and Culture Conditionsmentioning

confidence: 99%

“…The Bacilli are rod shaped gram positive bacteria, and characterized by spore forming ability and aerobic or facultative anaerobic metabolism [3]. Single spores are formed per cell in response to environmental stress, such as heat, cold, radiation or desiccation; features which support their existence in extreme habitats include desert sands, hot springs and Arctic soils.…”

Section: Introductionmentioning

confidence: 99%

Genomic analysis of a novel strain of Bacillus nealsonii, isolated from Surti buffalo rumen

Nathani¹,

Duggirala²,

Bhatt³

et al. 2014

ABB

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Whole-Genome Sequences of Bacillus subtilis and Close Relatives

Cited by 56 publications

References 18 publications

Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants

Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants

Transcriptional regulation of the l-lactate permease gene lutP by the LutR repressor of Bacillus subtilis RO-NN-1

Genomic analysis of a novel strain of Bacillus nealsonii, isolated from Surti buffalo rumen

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