Complete Genome Sequence of the Soil Actinomycete Kocuria rhizophila

ABSTRACT The soil actinomycete Kocuria rhizophila belongs to the suborder Micrococcineae, a divergent bacterial group for which only a limited amount of genomic information is currently available. K. rhizophila is also important in industrial applications; e.g., it is commonly used as a standard quality control strain for antimicrobial susceptibility testing. Sequencing and annotation of the genome of K. rhizophila DC2201 (NBRC 103217) revealed a single circular chromosome (2,697,540 bp; G+C content of 71.16%) containing 2,357 predicted protein-coding genes. Most of the predicted proteins (87.7%) were orthologous to actinobacterial proteins, and the genome showed fairly good conservation of synteny with taxonomically related actinobacterial genomes. On the other hand, the genome seems to encode much smaller numbers of proteins necessary for secondary metabolism (one each of nonribosomal peptide synthetase and type III polyketide synthase), transcriptional regulation, and lateral gene transfer, reflecting the small genome size. The presence of probable metabolic pathways for the transformation of phenolic compounds generated from the decomposition of plant materials, and the presence of a large number of genes associated with membrane transport, particularly amino acid transporters and drug efflux pumps, may contribute to the organism's utilization of root exudates, as well as the tolerance to various organic compounds.

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Biocontrol Using Bacillus amyloliquefaciens PP19 Against Litchi Downy Blight Caused by Peronophythora litchii

Frontiers in Microbiology ◽

10.3389/fmicb.2020.619423 ◽

2021 ◽

Vol 11 ◽

Author(s):

Li Zheng ◽

Shilian Huang ◽

Tom Hsiang ◽

Guohui Yu ◽

Dongliang Guo ◽

...

Keyword(s):

Bacillus Amyloliquefaciens ◽

Industrial Applications ◽

High Yield ◽

Large Chromosome ◽

Nucleotide Polymorphisms ◽

Industrial Strain ◽

Sod Activity ◽

Circular Chromosome ◽

Protein Coding ◽

Litchi Fruit

Bacillus amyloliquefaciens has been widely used in the agriculture, food, and medicine industries. Isolate PP19 was obtained from the litchi fruit carposphere and showed biocontrol efficacy against litchi downy blight (LDB) whether applied preharvest or postharvest. To further understand the underlying regulatory mechanisms, the genome of PP19 was sequenced and analyzed. The genome comprised a 3,847,565 bp circular chromosome containing 3990 protein-coding genes and 121 RNA genes. It has the smallest genome among 36 sequenced strains of B. amyloliquefaciens except for RD7-7. In whole genome phylogenetic analysis, PP19 was clustered into a group with known industrial applications, indicating that it may also produce high-yield metabolites that have yet to be identified. A large chromosome structural variation and large numbers of single nucleotide polymorphisms (SNPs) between PP19 (industrial strain) and UMAF6639 (plant-associated strain) were detected through comparative analysis, which may shed light on their functional differences. Preharvest treatment with PP19 enhanced resistance to LDB, by decreasing the plant H2O2 content and increasing the SOD activity. This is the first report of an industrial strain of B. amyloliquefaciens showing a plant-associated function and with major potential for the biocontrol of LDB.

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Discovery of anti-infective adipostatins through bioactivity-guided isolation and heterologous expression of a type III polyketide synthase

Bioorganic Chemistry ◽

10.1016/j.bioorg.2021.104925 ◽

2021 ◽

pp. 104925

Author(s):

Lukuan Hou ◽

Ying Li ◽

Qihao Wu ◽

Miyang Li ◽

Ethan A. Older ◽

...

Keyword(s):

Heterologous Expression ◽

Polyketide Synthase ◽

Type Iii Polyketide Synthase ◽

Type Iii

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A Fine Balancing Act of Type III Polyketide Synthase

Chemistry & Biology ◽

10.1016/j.chembiol.2004.09.001 ◽

2004 ◽

Vol 11 (9) ◽

pp. 1177-1178 ◽

Cited By ~ 1

Author(s):

Shiou-Chuan Tsai

Keyword(s):

Polyketide Synthase ◽

Type Iii Polyketide Synthase ◽

Type Iii

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Biosynthesis of Dictyostelium discoideum differentiation-inducing factor by a hybrid type I fatty acid–type III polyketide synthase

Nature Chemical Biology ◽

10.1038/nchembio811 ◽

2006 ◽

Vol 2 (9) ◽

pp. 494-502 ◽

Cited By ~ 86

Author(s):

Michael B Austin ◽

Tamao Saito ◽

Marianne E Bowman ◽

Stephen Haydock ◽

Atsushi Kato ◽

...

Keyword(s):

Fatty Acid ◽

Dictyostelium Discoideum ◽

Polyketide Synthase ◽

Type I ◽

Type Iii Polyketide Synthase ◽

Type Iii ◽

Hybrid Type ◽

Acid Type ◽

Fatty Acid Type

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In silico identification of Capsicum type III polyketide synthase genes and expression patterns in Capsicum annuum

Open Life Sciences ◽

10.1515/biol-2020-0077 ◽

2020 ◽

Vol 15 (1) ◽

pp. 753-762

Author(s):

Delong Kan ◽

Di Zhao ◽

Pengfei Duan

Keyword(s):

Molecular Mechanisms ◽

Polyketide Synthase ◽

Expression Patterns ◽

Class Ii ◽

Chili Pepper ◽

Type Iii Polyketide Synthase ◽

Type Iii ◽

Genes Encoding ◽

Duplication Events ◽

Pepper Leaves

AbstractStudies have shown that abundant and various flavonoids accumulate in chili pepper (Capsicum), but there are few reports on the genes that govern chili pepper flavonoid biosynthesis. Here, we report the comprehensive identification of genes encoding type III polyketide synthase (PKS), an important enzyme catalyzing the generation of flavonoid backbones. In total, 13, 14 and 13 type III PKS genes were identified in each genome of C. annuum, C. chinense and C. baccatum, respectively. The phylogeny topology of Capsicum PKSs is similar to those in other plants, as it showed two classes of genes. Within each class, clades can be further identified. Class II genes likely encode chalcone synthase (CHS) as they are placed together with the Arabidopsis CHS gene, which experienced extensive expansions in the genomes of Capsicum. Interestingly, 8 of the 11 Class II genes form three clusters in the genome of C. annuum, which is likely the result of tandem duplication events. Four genes are not expressed in the tissues of C. annuum, three of which are located in the clusters, indicating that a portion of genes was pseudogenized after tandem duplications. Expression of two Class I genes was complementary to each other, and all the genes in Class II were not expressed in roots of C. annuum. Two Class II genes (CA00g90790 and CA05g17060) showed upregulated expression as the chili pepper leaves matured, and two Class II genes (CA05g17060 and CA12g20070) showed downregulated expression with the maturation of fruits, consistent with flavonoid accumulation trends in chili pepper as reported previously. The identified genes, sequences, phylogeny and expression information collected in this article lay the groundwork for future studies on the molecular mechanisms of chili pepper flavonoid metabolism.

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Identification of a Polygonum cuspidatum three-intron gene encoding a type III polyketide synthase producing both naringenin and p-hydroxybenzalacetone

Planta ◽

10.1007/s00425-009-0899-1 ◽

2009 ◽

Vol 229 (5) ◽

pp. 1077-1086 ◽

Cited By ~ 13

Author(s):

Lan-Qing Ma ◽

Yan-Wu Guo ◽

Dong-Yao Gao ◽

Dong-Ming Ma ◽

You-Nian Wang ◽

...

Keyword(s):

Polyketide Synthase ◽

Polygonum Cuspidatum ◽

Gene Encoding ◽

Type Iii Polyketide Synthase ◽

Type Iii

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Complete Genome Sequence of the Wolbachia wAlbB Endosymbiont of Aedes albopictus

10.1101/415521 ◽

2018 ◽

Author(s):

Amit Sinha ◽

Zhiru Li ◽

Luo Sun ◽

Clotilde K. S. Carlow

Keyword(s):

Cell Line ◽

Aedes Albopictus ◽

Accession Number ◽

Pacbio Sequencing ◽

Particle Assembly ◽

Circular Chromosome ◽

Protein Coding ◽

Intracellular Symbiont ◽

Essential Components ◽

Genes Encoding

AbstractWolbachia, an alpha-proteobacterium closely related to Rickettsia is a maternally transmitted, intracellular symbiont of arthropods and nematodes. Aedes albopictus mosquitoes are naturally infected with Wolbachia strains wAlbA and wAlbB. Cell line Aa23 established from Ae. albopictus embryos retains only wAlbB and is a key model to study host-endosymbiont interactions. We have assembled the complete circular genome of wAlbB from the Aa23 cell line using long-read PacBio sequencing at 500X median coverage. The assembled circular chromosome is 1.48 megabases in size, an increase of more than 300 kb over the published draft wAlbB genome. The annotation of the genome identified 1,205 protein coding genes, 34 tRNA, 3 rRNA, 1 tmRNA and 3 other ncRNA loci. The long reads enabled sequencing over complex repeat regions which are difficult to resolve with short-read sequencing. Thirteen percent of the genome is comprised of IS elements distributed throughout the genome, some of which cause pseudogenization. Prophage WO genes encoding some essential components of phage particle assembly are missing, while the remainder are scattered around the genome. Orthology analysis identified a core proteome of 536 orthogroups across all completed Wolbachia genomes. The majority of proteins could be annotated using Pfam and eggNOG analyses, including ankyrins and components of the T4SS. KEGG analysis revealed the absence of 5 genes in wAlbB which are present in other Wolbachia. The availability of a complete circular chromosome from wAlbB will enable further biochemical, molecular and genetic analyses on this strain and related Wolbachia.Data depositionRaw data from PacBio sequencing have been deposited in the NCBI SRA database under BioProject accession number PRJNA454708, as runs SRR7784284, SRR7784285, SRR7784286, SRR7784287. The paired-end reads from Illumina library used for indel correction are available from NCBI SRA database as accession SRR7623731. The assembled genome and annotations have been submitted to the NCBI GenBank database with accession number CP031221.

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Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine

10.7287/peerj.preprints.2918v1 ◽

2017 ◽

Author(s):

Jacoline Gerritsen ◽

Bastian Hornung ◽

Bernadette Renckens ◽

Sacha A.F.T. van Hijum ◽

Vitor A.P. Martins dos Santos ◽

...

Keyword(s):

Amino Acids ◽

Small Intestine ◽

Short Chain Fatty Acids ◽

Limited Capacity ◽

Illumina Hiseq ◽

Circular Chromosome ◽

Protein Coding ◽

Mate Pair ◽

Simple Carbohydrates

Background. The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. Methods. The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired end, mate pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) while growing on three different carbohydrate sources and short chain fatty acids were measured via HPLC. Results. Hence, we present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed pinpointing the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides. Discussion. This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available and uncovered potential mechanisms for competition with mucus-degrading microbes.

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Complete Genome Sequence of Thiohalobacter sp. Strain COW1, Isolated from Activated Sludge Treating Coke Oven Wastewater

Microbiology Resource Announcements ◽

10.1128/mra.00013-21 ◽

2021 ◽

Vol 10 (7) ◽

Author(s):

Kentaro Miyazaki ◽

Hikaru Suenaga ◽

Mamoru Oshiki ◽

Shuichi Kawano ◽

Toshikazu Fukushima

Keyword(s):

Activated Sludge ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Coke Oven ◽

Rrna Genes ◽

Trna Genes ◽

Circular Chromosome ◽

Protein Coding ◽

Degrading Bacterium

ABSTRACT A thiocyanate-degrading bacterium, Thiohalobacter sp. strain COW1, was isolated from activated sludge treating coke oven wastewater, and the complete genome sequence was determined. COW1 contained a single circular chromosome (3.23 Mb; G+C content, 63.4%) in which 2,788 protein-coding genes, 39 tRNA genes, and 3 rRNA genes were identified.

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