Complete Genome Sequence of Latilactobacillus sp. Strain WDN19, a High- d- Aspartate-Producing Lactic Acid Bacterium Isolated from a Japanese Pickle

We report here the complete genome sequence of Latilactobacillus sp. strain WDN19, isolated from a Japanese pickle. This strain can produce a large amount of d- aspartate in the culture broth. The genome consists of a circular chromosome (1,967,462 bp; GC content, 41.88%) and a circular plasmid (66,648 bp; GC content, 35.08%).

Properties of polyplexes formed between a cationic polymer derived from L-arabinitol and nucleic acids

In this work a sugar-based cationic polymer derived from L-arabinitol, PUArab, was prepared and its interactions with the linear calf thymus DNA and with the circular plasmid pEGFP-C1 were investigated...

Complete Genome Sequencing Provides Novel Insight Into the Virulence Repertories and Phylogenetic Position of Dry Beans Pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens

Bacterial wilt of dry beans (family Fabaceae) caused by the actinobacterial agent Curtobacterium flaccumfaciens pv. flaccumfaciens is one of the most important diseases threatening edible legume production around the globe. Despite the economic losses due to the bacterial wilt disease, the pathogen has not so far been investigated for its genomic features, pathogenicity determinants, and virulence strategies. Here we present the first complete genome sequence of a highly virulent bacteriocin-producing C. flaccumfaciens pv. flaccumfaciens strain P990. The bacterium has a circular chromosome consisting of 3,736 kbp with the G+C% content of 71.0%. Furthermore, a 147-kbp circular plasmid (pCff1) with 66.1% G+C% content as well as two circular plasmid-like DNAs with sizes of 25 and 22 kbp were detected within the genomic contents of C. flaccumfaciens pv. flaccumfaciens. Phylogenetic analyses revealed that only a few number of Curtobacterium sp. strains deposited in the public databases could be classified within the species C. flaccumfaciens. Comparative genomics of C. flaccumfaciens pv. flaccumfaciens using the genome sequences of actinobacterial plant pathogens revealed the presence of a set of unique low G+C% content genomic islands in the C. flaccumfaciens pv. flaccumfaciens genome. Homologs of pathogenicity-determinant loci capable of producing 1,4-beta-xylanase (xysA), pectate lyase (pelA1 and pelA2), serine protease (chpC, chpG, and pat-1), and sortase (srtA) were detected in C. flaccumfaciens pv. flaccumfaciens genome. The genomic data presented here extend our understanding of the C. flaccumfaciens pv. flaccumfaciens genomic features and pave the ways of research on functional and interaction genetics to combat the risk of bacterial wilt disease in the 21st century’s dry bean industry.

Complete Genome Sequence of Sulfurospirillum Strain ACSTCE, a Tetrachloroethene-Respiring Anaerobe Isolated from Contaminated Soil

ABSTRACT Here, we report the complete genome sequence of the tetrachloroethene-to-trichloroethene dechlorinator Sulfurospirillum sp. strain ACSTCE. The genome consists of a 38.05-kb circular plasmid and a 2.69-Mb circular chromosome, which encodes 3 identical reductive dehalogenases with 91.47% amino acid identity to the PceA of Sulfurospirillum multivorans strain DSM 12446.

Intra-Molecular Homologous Recombination of Scarless Plasmid

Although many methods have been reported, plasmid construction compromises transformant efficiency (number of transformants per ng of DNAs) with plasmid accuracy (rate of scarless plasmids). An efficient method is two-step PCR serving DNA amplification. An accurate method is ExnaseII cloning serving homology recombination (HR). We combine DNA amplification and HR to develop an intra-molecular HR by amplifying plasmid DNAs to contain homology 5′- and 3′-terminus and recombining the plasmid DNAs in vitro. An example was to construct plasmid pET20b-AdD. The generality was checked by constructing plasmid pET21a-AdD and pET22b-AdD in parallel. The DNAs having 30-bp homology arms were optimal for intra-molecular HR, and transformation of which created 14.2 transformants/ng and 90% scarless plasmids, more than the two-step PCR and the ExnaseII cloning. Transformant efficiency correlated with the component of nicked circular plasmid DNAs of HR products, indicating nick modification in vivo leads to scar plasmids.

Complete Genome Sequence of Pseudomonas coronafaciens pv. oryzae 1_6

Pseudomonas coronafaciens pv. oryzae 1_6 was originally isolated as a phytopathogen of rice. Here, we report a complete genome sequence for this strain, containing a circular chromosome and one circular plasmid, assembled using a hybrid approach combining Illumina paired-end reads and longer reads sequenced on an Oxford Nanopore Flongle flow cell.

Complete Genome Sequence of Gordonia sp. 135, a Promising Dibenzothiophene- and Hydrocarbon-Degrading Strain

Gordonia sp. strain 135 is a promising dibenzothiophene-desulfurizing and hydrocarbon-degrading bacterium. It can utilize dibenzothiophene as the sole sulfur source. The genome of strain 135 was completely sequenced; it consists of a 5,039,827-bp circular chromosome and a 164,963-bp circular plasmid.

Liberibacter crescens Is a Cultured Surrogate for Functional Genomics of Uncultured Pathogenic ‘Candidatus Liberibacter’ spp. and Is Naturally Competent for Transformation

‘Candidatus Liberibacter’ spp. are uncultured insect endosymbionts and phloem-limited bacterial plant pathogens associated with diseases ranging from severe to nearly asymptomatic. ‘Ca. L. asiaticus’, causal agent of Huanglongbing or citrus “greening,” and ‘Ca. L. solanacearum’, causal agent of potato zebra chip disease, respectively threaten citrus and potato production worldwide. Research on both pathogens has been stymied by the inability to culture these agents and to reinoculate into any host. Only a single isolate of a single species of Liberibacter, Liberibacter crescens, has been axenically cultured. L. crescens strain BT-1 is genetically tractable to standard molecular manipulation techniques and has been developed as a surrogate model for functional studies of genes, regulatory elements, promoters, and secreted effectors derived from the uncultured pathogenic Liberibacters. Detailed, step-by-step, and highly reproducible protocols for axenic culture, transformation, and targeted gene knockouts of L. crescens are described. In the course of developing these protocols, we found that L. crescens is also naturally competent for direct uptake and homology-guided chromosomal integration of both linear and circular plasmid DNA. The efficiency of natural transformation was about an order of magnitude higher using circular plasmid DNA compared with linearized fragments. Natural transformation using a replicative plasmid was obtained at a rate of approximately 900 transformants per microgram of plasmid, whereas electroporation using the same plasmid resulted in 6 × 104 transformants. Homology-guided marker interruptions using either natural uptake or electroporation of nonreplicative plasmids yielded 10 to 12 transformation events per microgram of DNA, whereas similar interruptions using linear fragments via natural uptake yielded up to 34 transformation events per microgram of DNA.

Complete Genome Sequence of Marinobacter sp. Strain JH2, Isolated from Seawater of the Kiel Fjord

Here, we present the genome sequence of the Gram-negative and rod-shaped Marinobacter sp. strain JH2, which was isolated from seawater of the Kiel Fjord in Germany. The draft genome consists of two replicons, including one chromosome (3.6 Mb) and a circular plasmid (36.7 kb). The genome harbors 3,347 protein-coding genes.