Classification of the gifted natural product producerStreptomyces roseofacienssp. nov. by polyphasic taxonomy

ABSTRACTA novel verticillate strain of streptomycetes,Streptomycesstrain MBT76T, was isolated from the QinLing mountains, which harbours more than 40 biosynthetic gene clusters for natural products. Here we present full taxonomic classification of strain MBT76T, and show that it has chemotaxonomic, genomic and morphological properties consistent with its classification in the genusStreptomyces. Strain MBT76Tis part of the cluster of Streptoverticillates, a group within the genusStreptomycesthat has characteristic whorl-forming spores produced in chains along the lateral wall of the hyphae. Multi-locus sequence analysis based on five housekeeping gene alleles showed that MBT76Tis closely related toStreptomyces hiroshimensis. Average Nucleotide Identification (ANI) and Genome to Genome Distance Calculation (GGDC) of the genomes of strain MBT76TandS. hiroshimensisseparated them into distinct species. Strain MBT76Trepresents a novel species of the genusStreptomycesfor which we propose the nameStreptomyces roseofacienssp. nov. The type strain is MBT76T(=NCCB 100637T=DSM 106196T). The whole genome of MBT76Thas 7974 predicted open reading frames and a total genome size of 8.64 Mb. Further genomic analysis showed that verticillate streptomycetes lack the sporulation genessgE, and our data suggest that this is a useful genetic marker for the spore-chain morphology of the verticillates.

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Draft Genome Sequence of Saccharomonospora piscinae KCTC 19743T, an Actinobacterium Containing Secondary Metabolite Biosynthetic Gene Clusters

Microbiology Resource Announcements ◽

10.1128/mra.01588-19 ◽

2020 ◽

Vol 9 (15) ◽

Author(s):

Ninfa Ramírez-Durán ◽

Rafael R. de la Haba ◽

Blanca Vera-Gargallo ◽

Cristina Sánchez-Porro ◽

Scarlett Alonso-Carmona ◽

...

Keyword(s):

Genome Sequence ◽

Polyketide Synthase ◽

Draft Genome ◽

Gene Clusters ◽

Open Reading Frames ◽

Draft Genome Sequence ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Peptide Synthetase ◽

Reading Frames

The draft genome sequence of Saccharomonospora piscinae KCTC 19743T, with a size of 4,897,614 bp, was assembled into 11 scaffolds containing 4,561 open reading frames and a G+C content of 71.0 mol%. Polyketide synthase and nonribosomal peptide synthetase gene clusters, which are responsible for the biosynthesis of several biomolecules, were identified and located in different regions in the genome.

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Cloning of the Bisucaberin B Biosynthetic Gene Cluster from the Marine Bacterium Tenacibaculum mesophilum, and Heterologous Production of Bisucaberin B

Marine Drugs ◽

10.3390/md16090342 ◽

2018 ◽

Vol 16 (9) ◽

pp. 342 ◽

Cited By ~ 1

Author(s):

Masaki Fujita ◽

Yusuke Goto ◽

Ryuichi Sakai

Keyword(s):

Gene Cluster ◽

Marine Bacterium ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Open Reading Frames ◽

Linear Molecule ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Key Enzyme ◽

Reading Frames

The biosynthetic gene cluster for bisucaberin B (1, bsb gene cluster), an N-hydroxy-N-succinyl diamine (HSD)-based siderophore, was cloned from the marine bacterium Tenacibaculum mesophilum, originated from a marine sponge. The bsb gene cluster consists of six open reading frames (ORFs), in contrast to the four ORFs typically seen in biosynthetic gene clusters of the related molecules. Heterologous expression of the key enzyme, BsbD2, which is responsible for the final biosynthetic step of 1 resulted in production of bisucaberin B (1), but not bisucaberin (2) a macrocyclic counterpart of 1. To date, numbers of related enzymes producing macrocyclic analogues have been reported, but this work represents the first example of the HSD-based siderophore biosynthetic enzyme which exclusively produces a linear molecule rather than macrocyclic counterparts.

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Genome Sequence of Streptomyces cavourensis 1AS2a, a Rhizobacterium Isolated from the Brazilian Cerrado Biome

Microbiology Resource Announcements ◽

10.1128/mra.00065-19 ◽

2019 ◽

Vol 8 (18) ◽

Author(s):

Harold Alexander Vargas Hoyos ◽

Suikinai Nobre Santos ◽

Gabriel Padilla ◽

Itamar Soares Melo

Keyword(s):

Gene Clusters ◽

Antimicrobial Activities ◽

Open Reading Frames ◽

Biosynthetic Gene ◽

Brazilian Cerrado ◽

Neotropical Savanna ◽

Biosynthetic Gene Clusters ◽

Content Type ◽

Wheat Rhizosphere ◽

Reading Frames

Streptomyces cavourensis strain 1AS2a, isolated from wheat rhizosphere in the Brazilian Neotropical savanna, exhibits strong antimicrobial activities. Its genome comprises 7,600,475 bp with 6,590 open reading frames (ORFs) that reveal 30 biosynthetic gene clusters (BGCs).

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Genomic Analysis of Clostridium perfringens Bacteriophage φ3626, Which Integrates into guaA and Possibly Affects Sporulation

Journal of Bacteriology ◽

10.1128/jb.184.16.4359-4368.2002 ◽

2002 ◽

Vol 184 (16) ◽

pp. 4359-4368 ◽

Cited By ~ 57

Author(s):

Markus Zimmer ◽

Siegfried Scherer ◽

Martin J. Loessner

Keyword(s):

Clostridium Perfringens ◽

Attachment Site ◽

Genomic Analysis ◽

Gene Clusters ◽

Housekeeping Gene ◽

Bacterial Attachment ◽

Open Reading Frames ◽

Protein Profiling ◽

Specific Gene ◽

Major Life

ABSTRACT Two temperate viruses, φ3626 and φ8533, have been isolated from lysogenic Clostridium perfringens strains. Phage φ3626 was chosen for detailed analysis and was inspected by electron microscopy, protein profiling, and host range determination. For the first time, the nucleotide sequence of a bacteriophage infecting Clostridium species was determined. The virus belongs to the Siphoviridae family of the tailed phages, the order Caudovirales. Its genome consists of a linear double-stranded DNA molecule of 33,507 nucleotides, with invariable 3′-protruding cohesive ends of nine residues. Fifty open reading frames were identified, which are organized in three major life cycle-specific gene clusters. The genes required for lytic development show an opposite orientation and arrangement compared to the lysogeny control region. A function could be assigned to 19 gene products, based upon bioinformatic analyses, N-terminal amino acid sequencing, or experimental evidence. These include DNA-packaging proteins, structural components, a dual lysis system, a putative lysogeny switch, and proteins that are involved in replication, recombination, and modification of phage DNA. The presence of genes encoding a putative sigma factor related to sporulation-dependent sigma factors and a putative sporulation-dependent transcription regulator suggests a possible interaction of φ3626 with onset of sporulation in C. perfringens. We found that the φ3626 attachment site attP lies in a noncoding region immediately downstream of int. Integration of the viral genome occurs into the bacterial attachment site attB, which is located within the 3′ end of a guaA homologue. This essential housekeeping gene is functionally independent of the integration status, due to reconstitution of its terminal codons by phage sequence.

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Characterization and Genome Analysis of Staphylococcus aureus Podovirus CSA13 and Its Anti-Biofilm Capacity

Viruses ◽

10.3390/v11010054 ◽

2019 ◽

Vol 11 (1) ◽

pp. 54 ◽

Cited By ~ 9

Author(s):

Yoyeon Cha ◽

Jihwan Chun ◽

Bokyung Son ◽

Sangryeol Ryu

Keyword(s):

Staphylococcus Aureus ◽

Biocontrol Agent ◽

Genomic Analysis ◽

Open Reading Frames ◽

Experimental Setting ◽

Human Pathogens ◽

Bacteriophage Therapy ◽

Chromosomal Structure ◽

Inhibition Effect ◽

Reading Frames

Staphylococcus aureus is one of the notable human pathogens that can be easily encountered in both dietary and clinical surroundings. Among various countermeasures, bacteriophage therapy is recognized as an alternative method for resolving the issue of antibiotic resistance. In the current study, bacteriophage CSA13 was isolated from a chicken, and subsequently, its morphology, physiology, and genomics were characterized. This Podoviridae phage displayed an extended host inhibition effect of up to 23 hours of persistence. Its broad host spectrum included methicillin susceptible S. aureus (MSSA), methicillin resistant S. aureus (MRSA), local S. aureus isolates, as well as non-aureus staphylococci strains. Moreover, phage CSA13 could successfully remove over 78% and 93% of MSSA and MRSA biofilms in an experimental setting, respectively. Genomic analysis revealed a 17,034 bp chromosome containing 18 predicted open reading frames (ORFs) without tRNAs, representing a typical chromosomal structure of the staphylococcal Podoviridae family. The results presented here suggest that phage CSA13 can be applicable as an effective biocontrol agent against S. aureus.

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Bacteriophages LIMElight and LIMEzero of Pantoea agglomerans, Belonging to the “phiKMV-Like Viruses”

Applied and Environmental Microbiology ◽

10.1128/aem.00128-11 ◽

2011 ◽

Vol 77 (10) ◽

pp. 3443-3450 ◽

Cited By ~ 35

Author(s):

Evelien M. Adriaenssens ◽

Pieter-Jan Ceyssens ◽

Vincent Dunon ◽

Hans-Wolfgang Ackermann ◽

Johan Van Vaerenbergh ◽

...

Keyword(s):

Soil Samples ◽

Pantoea Agglomerans ◽

Open Reading Frames ◽

Human Pathogen ◽

Content Type ◽

Host Diversity ◽

Double Stranded Dna ◽

Opportunistic Human Pathogen ◽

Reading Frames

ABSTRACTPantoea agglomeransis a common soil bacterium used in the biocontrol of fungi and bacteria but is also an opportunistic human pathogen. It has been described extensively in this context, but knowledge of bacteriophages infecting this species is limited. Bacteriophages LIMEzero and LIMElight ofP. agglomeransare lytic phages, isolated from soil samples, belonging to thePodoviridaeand are the firstPantoeaphages of this family to be described. The double-stranded DNA (dsDNA) genomes (43,032 bp and 44,546 bp, respectively) encode 57 and 55 open reading frames (ORFs). Based on the presence of an RNA polymerase in their genomes and their overall genome architecture, these phages should be classified in the subfamily of theAutographivirinae, within the genus of the “phiKMV-like viruses.” Phylogenetic analysis of all the sequenced members of theAutographivirinaesupports the classification of phages LIMElight and LIMEzero as members of the “phiKMV-like viruses” and corroborates the subdivision into the different genera. These data expand the knowledge ofPantoeaphages and illustrate the wide host diversity of phages within the “phiKMV-like viruses.”

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An Umbra-related Virus Found in Vasconcellea X Heilbornii (Caricaceae)

10.21203/rs.3.rs-196384/v1 ◽

2021 ◽

Author(s):

Juan F Cornejo-Franco ◽

Francisco Flores ◽

Dimitre Mollov ◽

diego fernando quito-avila

Keyword(s):

Phylogenetic Analysis ◽

New Genus ◽

Complete Sequence ◽

Open Reading Frames ◽

Rna Dependent Rna Polymerase ◽

Sequence Comparisons ◽

Genomic Features ◽

Overlapping Open Reading Frames ◽

Reading Frames

Abstract The complete sequence of a new viral RNA from babaco (Vasconcellea x heilbornii) was determined. The genome consisted of 4,584 nucleotides organized in two non-overlapping open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus and a 1,843 -nt-long NCR at the 3’ terminus. Sequence comparisons of ORF 2 revealed homology to the RNA-dependent-RNA-polymerase (RdRp) of several umbra- and umbra-related viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported from papaya, citrus, opuntia, maize and sugarcane hosts. This clade shares a most recent ancestor with the umbraviruses but has different genomic features. The creation of a new genus, within the Tombusviridae, is proposed for the classification of these novel viruses.

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Genomic Assemblies of Members of Burkholderia and Related Genera as a Resource for Natural Product Discovery

Microbiology Resource Announcements ◽

10.1128/mra.00485-20 ◽

2020 ◽

Vol 9 (42) ◽

Author(s):

Alex J. Mullins ◽

Cerith Jones ◽

Matthew J. Bull ◽

Gordon Webster ◽

Julian Parkhill ◽

...

Keyword(s):

Natural Product ◽

Genome Mining ◽

Genomic Analysis ◽

Gene Clusters ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Natural Product Discovery

ABSTRACT The genomes of 450 members of Burkholderiaceae, isolated from clinical and environmental sources, were sequenced and assembled as a resource for genome mining. Genomic analysis of the collection has enabled the identification of multiple metabolites and their biosynthetic gene clusters, including the antibiotics gladiolin, icosalide A, enacyloxin, and cepacin A.

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Genomic analysis of siderophore β-hydroxylases reveals divergent stereocontrol and expands the condensation domain family

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1903161116 ◽

2019 ◽

Vol 116 (40) ◽

pp. 19805-19814 ◽

Cited By ~ 8

Author(s):

Zachary L. Reitz ◽

Clifford D. Hardy ◽

Jaewon Suk ◽

Jean Bouvet ◽

Alison Butler

Keyword(s):

Predictive Power ◽

Genome Mining ◽

Genomic Analysis ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Peptide Synthetase ◽

Condensation Domain

Genome mining of biosynthetic pathways streamlines discovery of secondary metabolites but can leave ambiguities in the predicted structures, which must be rectified experimentally. Through coupling the reactivity predicted by biosynthetic gene clusters with verified structures, the origin of the β-hydroxyaspartic acid diastereomers in siderophores is reported herein. Two functional subtypes of nonheme Fe(II)/α-ketoglutarate–dependent aspartyl β-hydroxylases are identified in siderophore biosynthetic gene clusters, which differ in genomic organization—existing either as fused domains (IβHAsp) at the carboxyl terminus of a nonribosomal peptide synthetase (NRPS) or as stand-alone enzymes (TβHAsp)—and each directs opposite stereoselectivity of Asp β-hydroxylation. The predictive power of this subtype delineation is confirmed by the stereochemical characterization of β-OHAsp residues in pyoverdine GB-1, delftibactin, histicorrugatin, and cupriachelin. The l-threo (2S, 3S) β-OHAsp residues of alterobactin arise from hydroxylation by the β-hydroxylase domain integrated into NRPS AltH, while l-erythro (2S, 3R) β-OHAsp in delftibactin arises from the stand-alone β-hydroxylase DelD. Cupriachelin contains both l-threo and l-erythro β-OHAsp, consistent with the presence of both types of β-hydroxylases in the biosynthetic gene cluster. A third subtype of nonheme Fe(II)/α-ketoglutarate–dependent enzymes (IβHHis) hydroxylates histidyl residues with l-threo stereospecificity. A previously undescribed, noncanonical member of the NRPS condensation domain superfamily is identified, named the interface domain, which is proposed to position the β-hydroxylase and the NRPS-bound amino acid prior to hydroxylation. Through mapping characterized β-OHAsp diastereomers to the phylogenetic tree of siderophore β-hydroxylases, methods to predict β-OHAsp stereochemistry in silico are realized.

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