Two tRNA gene clusters associated with rRNA operons rrnD and rrnE in Bacillus subtilis.

ABSTRACT Microbes produce a plethora of secondary (or specialized) metabolites that, although not essential for primary metabolism, benefit them to survive in the environment, communicate, and influence cell differentiation. Biosynthetic gene clusters (BGCs), responsible for the production of these secondary metabolites, are readily identifiable on bacterial genome sequences. Understanding the phylogeny and distribution of BGCs helps us to predict the natural product synthesis ability of new isolates. Here, we examined 310 genomes from the Bacillus subtilis group, determined the inter- and intraspecies patterns of absence/presence for all BGCs, and assigned them to defined gene cluster families (GCFs). This allowed us to establish patterns in the distribution of both known and unknown products. Further, we analyzed variations in the BGC structures of particular families encoding natural products, such as plipastatin, fengycin, iturin, mycosubtilin, and bacillomycin. Our detailed analysis revealed multiple GCFs that are species or clade specific and a few others that are scattered within or between species, which will guide exploration of the chemodiversity within the B. subtilis group. Surprisingly, we discovered that partial deletion of BGCs and frameshift mutations in selected biosynthetic genes are conserved within phylogenetically related isolates, although isolated from around the globe. Our results highlight the importance of detailed genomic analysis of BGCs and the remarkable phylogenetically conserved erosion of secondary metabolite biosynthetic potential in the B. subtilis group. IMPORTANCE Members of the B. subtilis species complex are commonly recognized producers of secondary metabolites, among those, the production of antifungals, which makes them promising biocontrol strains. While there are studies examining the distribution of well-known secondary metabolites in Bacilli, intraspecies clade-specific distribution has not been systematically reported for the B. subtilis group. Here, we report the complete biosynthetic potential within the B. subtilis group to explore the distribution of the biosynthetic gene clusters and to reveal an exhaustive phylogenetic conservation of secondary metabolite production within Bacillus that supports the chemodiversity within this species complex. We identify that certain gene clusters acquired deletions of genes and particular frameshift mutations, rendering them inactive for secondary metabolite biosynthesis, a conserved genetic trait within phylogenetically conserved clades of certain species. The overview guides the assignment of the secondary metabolite production potential of newly isolated Bacillus strains based on genome sequence and phylogenetic relatedness.

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Characterization and sequence analysis of potential biofertilizer and biocontrol agent Bacillus subtilis strain SEM-9 from silkworm excrement

Canadian Journal of Microbiology ◽

10.1139/cjm-2018-0350 ◽

2019 ◽

Vol 65 (1) ◽

pp. 45-58 ◽

Cited By ~ 4

Author(s):

Qingrong Li ◽

Sentai Liao ◽

Huyu Zhi ◽

Dongxu Xing ◽

Yang Xiao ◽

...

Keyword(s):

Bacillus Subtilis ◽

Fusarium Wilt ◽

Biocontrol Agent ◽

Gene Clusters ◽

Antagonistic Effect ◽

Subtilis Strain ◽

Fusarium Spp ◽

Antagonistic Microorganisms ◽

Biochemical Analyses ◽

Physiological And Biochemical

Fusarium wilt is a devastating soil-borne disease caused mainly by highly host-specific formae speciales of Fusarium oxysporum. Antagonistic microorganisms play a very important role in Fusarium wilt control, and the isolation of potential biocontrol strains is becoming more and more important. We isolated a bacterial strain (SEM-9) from the high-temperature stage of silkworm excrement composting, which had a marked ability to solubilize phosphorus, promote the growth and increase the yield of the small Chinese cabbage, and which also exhibited considerable antagonistic effect towards Fusarium sambucinum and other fungi. The result of physiological and biochemical analyses, as well as genome sequencing, showed that SEM-9 was a strain of Bacillus subtilis. Through genome annotation and analysis, it was found that SEM-9 contained genes related to the regulation of biofilm formation, which may play an important role in colonization, and gene clusters encoding the biosynthesis of antimicrobials, such as surfactin, bacilysin, fengycin, and subtilosin-A. The production of such antifungal compounds may constitute the basis of the mode-of-action of SEM-9 against Fusarium spp. These data suggested that the SEM-9 strain has potential as both a biofertilizer and a biocontrol agent, with the potential to manage Fusarium wilt disease in crops.

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Expression in Escherichia coli of Bacillus subtilis tRNA genes from a promoter within the tRNA gene region.

Journal of Bacteriology ◽

10.1128/jb.166.1.306-312.1986 ◽

1986 ◽

Vol 166 (1) ◽

pp. 306-312 ◽

Cited By ~ 3

Author(s):

B S Vold ◽

C J Green

Keyword(s):

Escherichia Coli ◽

Bacillus Subtilis ◽

Trna Gene ◽

Gene Region ◽

Trna Genes ◽

Expression In Escherichia Coli

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Structure and in vitro transcription of tRNA gene clusters containing the primers of MuLV reverse transcriptase

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1986.tb09772.x ◽

1986 ◽

Vol 158 (3) ◽

pp. 437-442 ◽

Cited By ~ 12

Author(s):

Tommaso RUSSO ◽

Francesco COSTANZO ◽

Adriana OLIVA ◽

Rosario AMMENDOLA ◽

Angela DUILIO ◽

...

Keyword(s):

Reverse Transcriptase ◽

Trna Gene ◽

Gene Clusters ◽

In Vitro Transcription

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Inducing secondary metabolite production of Aspergillus sydowii through microbial co-culture with Bacillus subtilis

10.21203/rs.3.rs-125911/v2 ◽

2021 ◽

Author(s):

Yu Sun ◽

Wen-Cai Liu ◽

Xuan Shi ◽

Hai-Zhou Zheng ◽

Zhi-Hui Zheng ◽

...

Keyword(s):

Bacillus Subtilis ◽

Gene Clusters ◽

Metabolite Profile ◽

Global Changes ◽

Aspergillus Sydowii ◽

Web Based ◽

New Approach ◽

Metabolite Profiles ◽

Natural Ecology ◽

Culture Strategy

Abstract Background: The co-culture strategy which mimics natural ecology by constructing an artificial microbial community is a useful tool to activate the biosynthetic gene clusters to generate new metabolites. However, the conventional method to study the co-culture is to isolate and purify compounds separated by HPLC, which is inefficient and time-consuming. Furthermore, the overall changes in the metabolite profile cannot be well characterized.Results: A new approach which integrates computational programs, MS-DIAL, MS-FINDER and web-based tools including GNPS and MetaboAnalyst, was developed to analyze and identify the metabolites of the co-culture of Aspergillus sydowii and Bacillus subtilis. A total of 25 newly biosynthesized metabolites were detected only in co-culture. The structures of the newly synthesized metabolites were elucidated, four of which were identified as novel compounds by the new approach. The accuracy of the new approach was confirmed by purification and NMR data analysis of 7 newly biosynthesized metabolites. The bioassay of newly synthesized metabolites showed that four of the compounds exhibited different degrees of PTP1b inhibitory activity, and compound N2 had the strongest inhibition activity with an IC50 value of 7.967 μM. Conclusions: Co-culture led to global changes of the metabolite profile and is an effective way to induce the biosynthesis of novel natural products. The new approach in this study is one of the effective and relatively accurate methods to characterize the changes of metabolite profiles and to identify novel compounds in co-culture systems.

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Reclassification of the biocontrol agents Bacillus subtilis BY-2 and Tu-100 as Bacillus velezensis and insights into the genomic and specialized metabolite diversity of the species

Microbiology ◽

10.1099/mic.0.000986 ◽

2020 ◽

Vol 166 (12) ◽

pp. 1121-1128 ◽

Cited By ~ 1

Author(s):

Alex J. Mullins ◽

Yinshui Li ◽

Lu Qin ◽

Xiaojia Hu ◽

Lihua Xie ◽

...

Keyword(s):

Bacillus Subtilis ◽

Natural Product ◽

Type Species ◽

Bacterial Species ◽

Gene Clusters ◽

Core Gene ◽

Biocontrol Agents ◽

Bacillus Velezensis ◽

Content Type ◽

Link Type

The genomes of two historical Bacillus species strains isolated from the roots of oilseed rape and used routinely in PR China as biocontrol agents to suppress Sclerotinia disease were sequenced. Average nucleotide identity (ANI) and digital DNA–DNA hybridization analyses demonstrated that they were originally misclassified as Bacillus subtilis and now belong to the bacterial species Bacillus velezensis . A broader ANI analysis of available Bacillus genomes identified 292 B. velezensis genomes that were then subjected to core gene analysis and phylogenomics. Prediction and dereplication of specialized metabolite biosynthetic gene clusters (BGCs) defined the prevalence of multiple antimicrobial-associated BGCs and highlighted the natural product potential of B. velezensis . By defining the core and accessory antimicrobial biosynthetic capacity of the species, we offer an in-depth understanding of B. velezensis natural product capacity to facilitate the selection and testing of B. velezensis strains for use as biological control agents.

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Genome mining and UHPLC-MS/MS illuminate the specificity of secondary metabolite synthetic gene clusters in Bacillus subtilis NCD-2

10.21203/rs.3.rs-33091/v1 ◽

2020 ◽

Author(s):

Zhenhe Su ◽

Xiuye Chen ◽

Xiaomeng Liu ◽

Qinggang Guo ◽

Shezeng Li ◽

...

Keyword(s):

Bacillus Subtilis ◽

Secondary Metabolites ◽

Secondary Metabolite ◽

Biological Activities ◽

Genome Mining ◽

Gene Clusters ◽

Synthetic Gene ◽

Integrative Approach ◽

Amino Acid Sequence Similarity ◽

Genetic Characteristics

Abstract Background Bacillus subtilisstrain NCD-2 is anexcellent biocontrol agent against plant soil-borne diseases and shows broad-spectrum antifungal activities. This study aimed to explore all the secondary metabolite synthetic gene clusters and related bioactive compounds in NCD-2. An integrative approach, which coupled genome mining with structural identification technologies using ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight tandem mass spectrometry (UHPLC-MS/MS), was conducted to interpret the chemical origins of the significant biological activities in NCD-2. Results Genome mining revealed that NCD-2 contained nine gene clustershaving predicted functionsinvolving secondary metabolites with bioactive abilities. They encoded six known products-fengycin, surfactin, bacillaene, subtilosin, bacillibactin, and bacilysin-as well as three unknown products.Interestingly, the synthetic gene clusters for surfactin and fengycin showed 83% and 92% amino acid sequence similarity levels with the corresponding productsin Bacillus velezensisstrain FZB42. A further comparison of gene clusters encoding fengycin and surfactinrevealed that strain NCD-2 had lost thefenC and fenDgenes in the fengycinbiosynthetic operon, and that the surfactin synthetic enzyme-related gene srfAB was divided into two parts.Abioinformatics analysis showed that fenEAmay function as fenCD in synthesizing fengycinand that the structure of thisfengycin synthetic gene clusteris likely unique to NCD-2.Five kinds of fengycin,with 26 homologs, and surfactin,with 4 homologs,were detectedfrom strain NCD-2, which indicated the non-typical and unique nature of this fengycin biosynthetic gene cluster.To the best of our knowledge, this is the first report of a non-typical gene cluster related to fengycin synthesis. Conclusions The data provide the genetic characteristics of secondary metabolite synthetic gene clusters for fengycinand surfactin in B. subtilis NCD-2, including the unique synthetic mechanism for fengycin, and suggest that bioactive secondary metabolites explain the biological activities of NCD-2.

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Draft Genome Sequence of Bacillus subtilis SB-14, an Antimicrobially Active Isolate from Namibian Social Spiders (Stegodyphus dumicola)

Microbiology Resource Announcements ◽

10.1128/mra.00156-19 ◽

2019 ◽

Vol 8 (25) ◽

Author(s):

Stine Sofie Frank Nielsen ◽

Simone Weiss ◽

Seven Nazipi ◽

Ian P. G. Marshall ◽

Trine Bilde ◽

...

Keyword(s):

Bacillus Subtilis ◽

Genome Sequence ◽

Draft Genome ◽

Gene Clusters ◽

Draft Genome Sequence ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

High Quality ◽

Social Spider ◽

Content Type

We present the high-quality draft genome sequence of Bacillus subtilis SB-14, isolated from the Namibian social spider Stegodyphus dumicola. In accordance with its antimicrobial activity, both known and potentially novel antimicrobial biosynthetic gene clusters were identified in the genome of SB-14.

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Nonribosomal Peptide Synthase Gene Clusters for Lipopeptide Biosynthesis in Bacillus subtilis 916 and Their Phenotypic Functions

Applied and Environmental Microbiology ◽

10.1128/aem.02921-14 ◽

2014 ◽

Vol 81 (1) ◽

pp. 422-431 ◽

Cited By ~ 49

Author(s):

Chuping Luo ◽

Xuehui Liu ◽

Huafei Zhou ◽

Xiaoyu Wang ◽

Zhiyi Chen

Keyword(s):

Bacillus Subtilis ◽

Antifungal Activity ◽

Hemolytic Activity ◽

Biofilm Formation ◽

Gene Clusters ◽

Colony Morphology ◽

Swarming Motility ◽

Nonribosomal Peptide ◽

Content Type ◽

Phenotypic Features

ABSTRACTBacilluscyclic lipopeptides (LPs) have been well studied for their phytopathogen-antagonistic activities. Recently, research has shown that these LPs also contribute to the phenotypic features ofBacillusstrains, such as hemolytic activity, swarming motility, biofilm formation, and colony morphology.Bacillus subtilis916 not only coproduces the three families of well-known LPs, i.e., surfactins, bacillomycin Ls (iturin family), and fengycins, but also produces a new family of LP called locillomycins. The genome ofB. subtilis916 contains four nonribosomal peptide synthase (NRPS) gene clusters,srf,bmy,fen, andloc, which are responsible for the biosynthesis of surfactins, bacillomycin Ls, fengycins, and locillomycins, respectively. By studyingB. subtilis916 mutants lacking production of one, two, or three LPs, we attempted to unveil the connections between LPs and phenotypic features. We demonstrated that bacillomycin Ls and fengycins contribute mainly to antifungal activity. Although surfactins have weak antifungal activityin vitro, the strain mutated insrfAAhad significantly decreased antifungal activity. This may be due to the impaired productions of fengycins and bacillomycin Ls. We also found that the disruption of any LP gene cluster other thanfenresulted in a change in colony morphology. While surfactins and bacillomycin Ls play very important roles in hemolytic activity, swarming motility, and biofilm formation, the fengycins and locillomycins had little influence on these phenotypic features. In conclusion,B. subtilis916 coproduces four families of LPs which contribute to the phenotypic features ofB. subtilis916 in an intricate way.

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Chromosomal regions which control sporulation in Bacillus subtilis

Canadian Journal of Microbiology ◽

10.1139/m69-137 ◽

1969 ◽

Vol 15 (7) ◽

pp. 787-790 ◽

Cited By ~ 6

Author(s):

Marvin Rogolsky

Keyword(s):

Bacillus Subtilis ◽

Linkage Group ◽

Genetic Map ◽

Gene Clusters ◽

Linkage Groups ◽

The Third ◽

The Right

Large quantities of sporulation mutants have been isolated with a variety of mutagens. The genetic sites for asporogeny have been localized on the chromosome of Bacillus subtilis through transduction with phage PBSI. Through these procedures specific portions of the chromosome which are associated with sporulation have been identified. Although asporogenic (Sp−) defects were observed to be scattered throughout the four linkage groups of the genetic map of B. subtilis, only three extensive Sp− linkage groups were identified. The first linkage group of Sp− markers is located at the proximal end of the chromosome between the cys A and ery markers. The second cluster of spore genes mapped to the right of ura, and the third linkage group of spore markers mapped to the left of lys-2. Defects within specific regions of the first and third spore gene clusters obstructed some early products of sporogenesis.

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