Characterization of a Rolling-Circle Replication Plasmid pLR1 from Lactobacillus plantarum LR1

Characterization and sequencing analysis of pLP2.5-11 and pLP3.0-4 novel cryptic plasmids from Lactiplantibacillus plantarum WP72/27

We sequenced and described two cryptic plasmids from Lactiplantibacillus plantarum strain WP72/27, termed pLP2.5-11 (OP831909) and pLP3.0-4 (OP831910). Nucleotide sequencing gave the sizes of pLP2.5-11 and pLP3.0-4 as 2754 and 3197 base pairs, with G + C contents 38.89% and 40.88% and predicted two and eight putative open reading frames, respectively. The RepA protein of pLP2.5-11 shared a 99% identity with pC30il, pLP1 and pC30il, whereas the RepB protein of pLP3.0-4 shared a 98% identity with pXY3, a member of the rolling-circle replication (RCR) pC194 family. The origin of plasmid replication was predicted to consist of inverted and directed repeat sequences upstream of the Rep genes. Sequence analysis predicted that both pLP2.5-11 and pLP3.0-4 plasmids replicate via a rolling-circle process.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03684-y.

Complete genome sequencing of Lactobacillus plantarum CAUH2 reveals a novel plasmid pCAUH203 associated with oxidative stress tolerance

Lactobacillus plantarum is remarkably adaptable to diverse habitats and is widely used in food industry. In this study, the genome sequence of L. plantarum CAUH2 was analyzed and compared with other L. plantarum genome sequences. A comparison of the genome sequence of CAUH2 to L. plantarum ST-III reveals that the similarity of these two genomes reached up to 99% identity with 98% coverage, but the plasmid profiles of CAUH2 and ST-III are different. Notably, plasmid pCAUH203 in L. plantarum CAUH2 harbors seven genes involved in oxidative stress response, such as genes encoding thioredoxin-disulfide reductase, thioredoxin and DNA protection protein. Due to plasmid pCAUH203, the thioredoxin reductase activity of CAUH2 was 2.1-fold higher than that of ST-III. When exposed to 5 mM H₂O₂, this activity was further increased to 9.87 ± 1.60 mU per mg protein in CAUH2, which was 2.7-fold higher than that of ST-III, indicating that thioredoxin antioxidant system encoded by pCAUH203 might contribute to the H₂O₂ resistance. This hypothesis was further confirmed by survival assay under 10 mM H₂O₂ stress. The survival rate of CAUH2 was 12-fold higher than that of ST-III. Therefore, the complete genome sequencing of L. plantarum CAUH2 provides new insights into the molecular mechanism of its oxidative stress resistance.

Characterization of a Rolling-Circle Replication Plasmid pM411 from Lactobacillus plantarum 1-3

A cryptic plasmid pM411 isolated from Lactobacillus plantarum 1-3 consisted of a 2303-bp circular molecule with a G + C content 32.96 %. Sequence analysis of pM411 revealed four putative open reading frames (ORFs). ORF1 shared 99 and 94 % similarities, respectively, with the Rep proteins of plasmids pLC2 and pYC2, which belong to the rolling-circle replication pMV158 family. A typical pMV158 family double-strand origin (dso) and a putative single-strand origin (sso) located upstream of the rep gene. Southern hybridization confirmed the presence of single-strand DNA (ssDNA) intermediates, suggesting that pM411 belongs to the RCR pMV158 family. Sequence homology analysis indicated that the sso belongs to the ssoW family. Furthermore, the relative copy number of pM411 was about 88 copies in each cell by real-time PCR.

Sequence analysis of five endogenous plasmids isolated from Lactobacillus pentosus F03

Lactobacillus pentosus F03, a strain isolated from pig intestines in Taiwan, contains multiple endogenous plasmids. We isolated, completely sequenced, and characterized five of the plasmids present in L. pentosus F03 designated as pF03-1 (3282bp), pF03-2 (3293bp), pF03-3 (1787bp), pF03-4 (2138bp), and pF03-5 (1949bp). The replication types of these plasmids were predicted by comparing the features of the replicon nucleotides and the similarity of replication proteins with those of the plasmids of known replication types. The results of basic local alignment search tool analyses indicate that these plasmids, except for pF03-4, belong to different replicating plasmid families. According to replicon and initiator protein analyses, pF03-1, pF03-2, and pF03-3, were determined to belong respectively to the pMV158, pC194/pUB110, and pT181 families of rolling-circle replication plasmids. However, pF03-5 contains the typical features observed in the family of theta-replicating plasmids and belongs to the pUCL287 family of theta-replicating plasmids.

Plasmids from Food Lactic Acid Bacteria: Diversity, Similarity, and New Developments

Plasmids are widely distributed in different sources of lactic acid bacteria (LAB) as self-replicating extrachromosomal genetic materials, and have received considerable attention due to their close relationship with many important functions as well as some industrially relevant characteristics of the LAB species. They are interesting with regard to the development of food-grade cloning vectors. This review summarizes new developments in the area of lactic acid bacteria plasmids and aims to provide up to date information that can be used in related future research.

Isolation and partial characterization of a bacteriocin produced by Lactobacillus plantarum BM-1 isolated from a traditionally fermented Chinese meat product

Lactobacillus plantarum BM-1 isolated from a traditionally fermented Chinese meat product was found to produce a novel bacteriocin that is active against a wide range of gram-positive and gram-negative bacteria. Production of the bacteriocin BM-1 started early in the exponential phase and its maximum activity (5120 AU/mL) was recorded early during the stationary phase (16 hr). Bacteriocin BM-1 is sensitive to proteolytic enzymes but stable in the pH range of 2.0-10.0 and heat-resistant (15 min at 121°C). This bacteriocin was purified through pH-mediated cell adsorption-desorption and cation-exchange chromatography on an SP Sepharose Fast Flow column. The molecular weight of the purified bacteriocin BM-1 was determined to be 4638.142 Da by electrospray ionization Fourier transform mass spectrometry. Furthermore, the N-terminal amino acid sequence was obtained through automated Edman degradation and found to comprise the following 15 amino acid residues: H2 N-Lys-Tyr-Tyr-Gly-Asn-Gly-Val-Tyr-Val-Gly-Lys-His-Ser-Cys-Ser. Comparison of this sequence with that of other bacteriocins revealed that bacteriocin BM-1 contains the consensus YGNGV amino acid motif near the N-terminus. Based on its physicochemical characteristics, molecular weight, and N-terminal amino acid sequence, plantaricin BM-1 is a novel class IIa bacteriocin.

Characterization of pR18, a novel rolling-circle replication plasmid from Lactobacillus plantarum

Lactobacillus plantarum PA18, a strain originally isolated from the leaves of Pandanus amaryllifolius, contains a pR18 plasmid. The pR18 plasmid is a 3211bp circular molecule with a G+C content of 35.8%. Nucleotide sequence analysis revealed two putative open reading frames, ORF1 and ORF2, in which ORF2 was predicted (317 amino acids) to be a replication protein and shared 99% similarity with the Rep proteins of pLR1, pLD1, pC30il, and pLP2000, which belong to the RCR pC194/pUB110 family. Sequence analysis also indicated that ORF1 was predicted to encode linA, an enzyme that enzymatically inactivates lincomycin. The result of Southern hybridization and mung bean nuclease treatment confirmed that pR18 replicated via the RCR mechanism. Phylogenetic tree analysis of pR18 plasmid proteins suggested that horizontal transfer of antibiotic resistance determinants without genes encoding mobilization has not only occurred between Bacillus and Lactobacillus but also between unrelated bacteria. Understanding this type of transfer could possibly play a key role in facilitating the study of the origin and evolution of lactobacillus plasmids. Quantitative PCR showed that the relative copy number of pR18 was approximately 39 copies per chromosome equivalent.

Characterization of pLP18, a novel cryptic plasmid of Lactobacillus plantarum PC518 isolated from Chinese pickle

A cryptic plasmid of Lactobacillus plantarum PC518 isolated from Chinese pickle, designated pLP18, was sequenced and characterized. It is a 1806-bp circular molecule with a G+C content of 37.5%. Sequence analysis of pLP18 revealed three putative open reading frames (ORFs), in which ORF1 contained conserved motifs of pMV158-family Rep proteins and showed 60% similarity with the Rep protein of pPSC22, a member of rolling-circle replication (RCR) pMV158 family. The double strand origin (dso) of pMV158 family and the single strand origin A (ssoA) located upstream of the rep gene. The putative cop and rnaII genes were predicted to be regulatory genes controlling copy number of pLP18. The results of Southern hybridization suggested that pLP18 replicate via the RCR mechanism. Furthermore, the relative copy number of pLP18 was estimated to be about 24 copies per chromosome equivalent by quantitative PCR.

Characterization of a rolling-circle replication plasmid pXY3 from Lactobacillus plantarum XY3

The complete nucleotide sequence of cryptic plasmid pXY3 isolated from Lactobacillus plantarum strain XY3 has been determined. It consisted of a 2968-bp circular molecule with a G+C content of 39%. Sequence analysis of pXY3 revealed three putative open reading frames (ORFs). Based on sequence similarity, the Rep protein shared 89% and 88% identity with Rep proteins of pLF24 and pWCFS102, respectively, which belonged to the rolling-circle replication (RCR) pMV158 family. A ssoT-like single-strand origin (sso) and a typical pMV158 family double-strand origin (dso) located upstream of the rep gene. Southern blot analysis indicated pXY3 replicate via a rolling-circle (RC) mechanism. Furthermore, the relative copy number of pXY3 was estimated to be about 97 copies per chromosome equivalent by real-time PCR.

Functional analysis of the plasmid pM4 replicon from Lactobacillus plantarum M4: determination of the minimal replicon and functionality identification of the putative sso

In order to determine the minimal replicon and the single strand origin (sso) of the plasmid pM4, different fragments of pM4 were amplified by polymerase chain reaction (PCR) and cloned into pBEm, a replication probe vector for Lactobacillus. The deletion analysis results showed that the minimal replicon of pM4 could be determined within a 1280bp fragment consisting of double strand origin (dso) and rep gene encoding replication protein. Based on plasmid segregation stability assay and its ability to convert single-stranded DNA (ssDNA) to double-stranded DNA (dsDNA) by Southern hybridization, an sso of replication was located at nucleotides -118-92 in the plasmid pM4, about 300bp upstream of dso. In addition, the host range assay indicated that plasmid pM4 could replicate in L. casei 05-21, L. rhamnosus AS 1.2466(T) and L. plantarum 05-19 of all the tested Lactobacillus strains. Analysis of the pM4 replicon will allow its use in constructing a food-grade vector for application in food industry.