Application based nucleotides of Lactobacillus rhamnosus to prepare a composition for anti-lipogenesis

An application based on nucleotide fragments of Lactobacillus rhamnosus GM-020, to prepare a composition for anti-lipogenesis. The Lactobacillus rhamnosus GM-020 was deposited on Dec. 18, 2003 and has the CCTCC designation number CCTCC M203098. Also provided is a composition containing Lactobacillus rhamnosus GM-020 or nucleotide fragments thereof as effective ingredients for anti-lipogenesis.

1. 11. A method of preparing a pharmaceutical composition comprising adding SEQ ID No. and/or and SEQ ID No. 5 to a composition comprising a pharmaceutical excipient and/or a pharmaceutical vehicle.
2. 22. A method of inhibiting lipid droplet formation in adipocytes in vitro comprising the administration of a composition comprising SEQ ID No. 1 and/or SEQ ID No. 5.
3. 33. A method of inhibiting the expression of fatty acid synthase (FAS) in adipocytes in vitro comprising the administration of a composition comprising SEQ ID No. 1 and/or SEQ ID No. 5.

CROSS-REFERENCE TO RELATED APPLICATIONS
The present application claims priority of Application No. 113104601, filed in Taiwan, R.O.C. on Feb. 6, 2024 under 35 U.S.C. § 119, the entire contents of all of which are hereby incorporated by reference.
REFERENCE TO AN ELECTRONIC SEQUENCE LISTING
The content of the electronic sequence listing (PB20230480_sequence.xml; Size: 12,986 bytes; and Date of Creation: Jan. 21, 2026) is herein incorporated by reference in its entirety.
BACKGROUND OF THE INVENTION
Brief Discussion of the Related Art
The effect of L. rhamnosus on regulation of adipogenesis had been verified in recent research. For example, the benefits of calcium ions for anti-obesity, inhibiting generation of the adipose tissue and more lipid oxidation in muscles, can be consolidated with fermented milk containing L. rhamnosus GG ingested. Moreover, L. rhamnosus 86 proves effective in inhibiting differentiation of adipocytes as well as lipogenesis and correcting obesity attributed to fat-rich diets. However, the functions of L. rhamnosus engaging in fat reduction and regulating the anti-obesity mechanism still need to be clarified by more evidence. Excessive lipid accumulation is attributed to two dysfunctional mechanisms: (1) excessive lipogenesis; (2) fatty acid oxidation or lipodieresis impaired. Reportedly, genes such as FAS (Fatty acid synthase), ACC (acetyl coenzymeA carboxylase), SREBP1 (sterol regulatory element-binding transcription factor) and SCD1 (stearoyl coenzymeA desaturase 1), all of which are classified as lipogenesis-related genes, feature over-expression of genes/proteins promoting lipogenesis.
In the whole genome sequence of a bacterium, some oligodeoxynucleotide (ODN) fragments are characteristic of the physiological effect for immunoregulation. For example, the copy number of TTAGGG (SEQ ID NO. 10) and TCAAGCTTGA (SEQ ID NO. 12) in Lactobacillus paracasei is higher than the number of pathogenic bacteria or Escherichia coli and ODN synthesized based on the sequences contributes to inhibiting activation of dendritic cells in the intestinal lamina propria (Bouladoux et al.). Moreover, the sequence of TTTCGTTT (SEQ ID NO. 11) presented in L. rhamnosus GG has effects on immune stimulation, such as B cells proliferation and Th1 activation. As shown in arthritis of mice, the sequence of CCTCAAGCTTGAGGGG (SEQ ID NO. 13) features anti-inflammation and corrects serious arthritis significantly. However, there is no report of CpG-ODNs in probiotics engaging in regulation of lipogenesis.
Accordingly, how to find oligodeoxynucleotide fragments in probiotics with the function of regulating lipogenesis is the issue explored in the present disclosure.
FIELD OF THE INVENTION
The present disclosure relates to nucleotides of Lactobacillus rhamnosus, as known as Lacticaseibacillus rhamnosus, for anti-lipogenesis, this is effectuated by inhibiting generation of lipid droplets in adipocytes particularly.
BRIEF SUMMARY OF THE INVENTION
After years of research and considering the issues mentioned above, the patent inventor has separated oligodeoxy nucleotide (ODN) fragments of probiotics, Lactobacillus rhamnosus, for anti-lipogenesis effectively as a novel and safe preventive measure for obesity attributed to fat-rich diets.
To this end, the present invention discloses a nucleotide which is effective in anti-lipogenesis and given SEQ ID NO: 1 as the sequence number.
The present invention also discloses a nucleotide which is effective in anti-lipogenesis and given SEQ ID NO: 5 as the sequence number.
The present invention further discloses a composition contributing to anti-lipogenesis and containing Lactobacillus rhamnosus GM-020, or nucleotide fragments thereof, as effective ingredients. Lactobacillus rhamnosus GM-020 was deposited on Dec. 18, 2003 and has the CCTCC designation number CCTCC M203098, and the nucleotide fragments contain the sequence of SEQ ID NO. 1 or SEQ ID NO. 5.
In one embodiment of the present disclosure, the composition is taken as a pharmaceutical composition, a nutritional supplement, or healthcare food.
In one embodiment of the present disclosure, the composition further comprises pharmaceutically acceptable vehicles.
In one embodiment of the present disclosure, the composition is a solution, a suspension liquid, an emulsion, powders, a pastille, a pill, syrup, an oral ingot, a tablet, a chewing gum, a thick juice, or a capsule.
In one embodiment of the present disclosure, the composition further comprises an editable material selected from water, a fluid dairy product, milk, condensed milk, a yogurt, a frozen yogurt, a lactic acid fermented beverage, milk powders, an ice cream, a cream, a cheese, soy milk, fermented soy milk, a vegetable juice, a fruit juice, a sports drink, a dessert, a jelly, a confection, baby food, healthcare food, an animal fodder, a Chinese herbal medicine, or a dietary supplement.
The present invention further discloses an application based on nucleotide fragments of Lactobacillus rhamnosus GM-020, to prepare a composition featuring anti-lipogenesis and containing Lactobacillus rhamnosus GM-020, or nucleotide fragments thereof as effective ingredients. Lactobacillus rhamnosus GM-020 was deposited on Dec. 18, 2003 and has the CCTCC designation number CCTCC M203098, and the nucleotide fragments contain the sequence of SEQ ID NO. 1 or SEQ ID NO. 5. In one embodiment of the present disclosure, the anti-lipogenesis means inhibition of lipid droplets generated in adipocytes.
In one embodiment of the present disclosure, the anti-lipogenesis is effectuated by reducing expression of the lipogenesis-related gene, FAS, inside adipocytes.
In the present disclosure, the effects of some specific oligodeoxynucleotide fragments, that is, IM1: TTAGGG (SEQ ID NO. 10), IM2: TTTCGTTT (SEQ ID NO. 11) and IM3: TCAAGCTTGA (SEQ ID NO. 12) as objects of analyses, of Lactobacillus rhamnosus, GM-020, on inhibition of lipogenesis were accessed. Moreover, the effects of five ODN fragments, each of which contained the core sequence, IM3, on inhibition of lipogenesis were tested in experiments. As shown in test results, GM-020 containing two specific oligodeoxynucleotide fragments proved effective in inhibiting lipogenesis significantly. In the present disclosure, the composition with probiotics or nucleotides as an effective ingredient has the advantageous characteristic of low side effects and can be taken as a novel and safe preventive measure for obesity attributed to fat-rich diets.
Further scope of the applicability of the present invention will become apparent from the detailed description given hereinafter. However, it should be understood that the detailed description and specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.



BRIEF DESCRIPTION OF THE DRAWINGS
The present invention will become more fully understood from the detailed description given hereinbelow and the accompanying drawings which are given by way of illustration only, and thus are not limitative of the present invention.
FIG. 1A illustrates circular genome data of the whole genome of GM-020.
FIG. 1B illustrates functional analyses of the whole genome of GM-020.
FIG. 1C illustrates sequencing analyses of GM-020.
FIG. 1D illustrates speciational evolution of GM-020.
FIG. 1E illustrates speciational evolution of GM-020.
FIG. 2A illustrates the effect of IM3-1 on inhibiting lipid droplets generated.
FIG. 2B illustrates the effect of IM3-5 on inhibiting lipid droplets generated.
FIG. 3 illustrates no effect of IM3-2, IM3-3 or IM3-4 on inhibiting lipid droplets generated.
FIG. 4 illustrates the effect of IM3-1 or IM3-5 on inhibiting gene expression of FAS.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
The technical and scientific terminologies in the patent specification are well known to persons with common knowledge in the art unless otherwise specified.
A singular noun joined by “a/an,” “one,” or “the” in the patent specification or claims may refer to more than one object unless otherwise specified.
Words like “or” or “and” refer to “and/or” unless otherwise specified. Moreover, words like “comprise” or “contain” are open-ended terms. The descriptions in a previous section refer to general involvement but are not interpreted as restrictions to the subject of the present invention.
The effective ingredients or the composition in the present disclosure, as well as at least a pharmaceutically acceptable vehicle, can be chosen by a person with common and well-known knowledge in the art for preparation of a formulation applicable to the composition. The formulation includes, without limitation, a solution, an emulsion, a suspension liquid, powders, a pastille, an oral ingot, a tablet, a chewing gum, a capsule, and another similar formulation applicable to the present invention.
The terminology of “pharmaceutically acceptable” means a substance or a composition and other components of a pharmaceutical concoction thereof being compatible with each other but not aggravating a patient's symptoms.
The terminology of “pharmaceutically acceptable vehicle” comprises one or more types of ingredients selected from: a solvent, an emulsifier, a suspension agent, a decomposing agent, a binding agent, an excipient, a stabilizing agent, a chelating agent, a diluent, a gelling agent, a preservative, a lubricating agent, a surfactant, and another similar vehicle applicable to the present invention.
One or more co-solvents, buffer agents, coloring agents, and flavoring agents common in the pharmaceutical industry can be discretionarily added in the composition as required.
The terminology of “pharmaceutical composition” means a solid or liquid composition with a form, concentration, and purity applicable to medicine administration for a patient from whom an expected physiological change is induced after administration. The pharmaceutical composition is sterile and/or non-pyrogenic.
The materials used in the patent specification are substances commercially available unless otherwise specified. Lactobacillus rhamnosus (also known as Lacticaseibacillus rhamnosus) GM-020, in an embodiment hereinafter, was deposited on Dec. 18, 2003 and has the designation number of CCTCC M203098 at the China Center for Type Culture Collection (CCTCC).
Embodiment 1, Whole Genome Sequencing of GM-020
Culturing and Sequencing of Probiotics
0.1 ml lactobacilli in 1 ml lactobacilli cultured overnight was instilled into 10 ml MRS broths for activation of second-generation strains and observation of the growth curve. After OD600 of 0.8 was detected, 3 ml Lactobacillus broths were flushed twice with filtered sterile water (13,000 rpm; 1 min) and Lactobacilli remained were prepared for genomic DNA extraction. DNAs were extracted with QIAGEN DNeasy® Blood & Tissue Kit (QIAGEN; Cat. No. 69504). The quality of genomic DNAs was checked through the Qubit fluorometer, the nanophotometer, and agarose gels. The whole-genome DNA sequencing was done by Health GeneTech Corp. DNAs to be tested were sequenced with Illumina Hiseq 2000 (for next generation sequencing) and Nanopore GridION (for third generation sequencing), respectively.
Pretreatment of Sequence Assembly:
Low-quality noises inside sequencing data were filtered with FASTX-Toolkit and MinIONQC (Quality Value=20, that is, error rate per base= 1/100) before sequence assembly, respectively.
Sequence Assembly and Correction of Sequencing Data:
The nucleotide sequences of the filtered high-quality second-generation sequencing short fragments and the third-generation sequencing data were assembled to be the longer continuous sequences with a published tool, MaSuRCA v3.3.1, based on the hybrid assembly method. The bridging sequences constructed were aligned based on the sequences of third-generation sequencing data for verification of the precedence relationship between contigs. Moreover, the variation test and the genome assembly improvement were completed by Pilon. With the Nanopore long-read sequence taken as a reference sequence, each discrepancy or gap of a single base in one reading was checked and corrected after short-read sequence alignment for reducing false positive.
Speciational Evolution Analysis, Sequencing Genome Annotation and Functional Pathway Analysis:
The sequence of a subtype strain collected after the sequence assembly and the sequence to be tested were checked during the multiple sequence alignment as a critical reference for completing the molecular evolution analysis, the evolutionary analysis, and traceability and facilitating rapid and accurate strain identification on the next-generation sequencing platform. The genome annotation was completed with several tools: Prokka for gene prediction of the whole genome of a procaryotic organism including protein coding and non-coding regions; Plasflow for plasmid identification; PHASTER for filtration of a phagore region inside a genome; Bagel4 & CARD for predictions of both genes correlated with generation of bacteriocin and probable drug resistance regions; eggNOG as one tool facilitating functional classifications on a region of functional proteins probably translated from a protein coding region and combined with the Cluster of Orthologous Genes (COG) of the protein database for annotations and classifications.
According to data analyses of the whole genome, genetic information and the phylogenetic tree, GM-020 is recognized as Lactobacillus rhamnosus and characteristic of the genome size of 3,037,161 bp. The whole genome, the functional analyses and the speciational evolution correlated with GM-020 are shown in FIG. 1A, FIG. 1B, FIG. 1C, FIG. 1D and FIG. 1E.
The frequency of IM1 (TTAGGG) (SEQ ID NO. 10), IM2 (TTTCGTTT) (SEQ ID NO. 11), and IM3 (TCAAGCTTGA) (SEQ ID NO. 12) sequences appearing in the whole genome were further analyzed in GM-020 and three other Lactobacillus rhamnosus strains, 4B15, DSM14870 and BPL5, as disclosed in published literature.
As summarized in Table 1, the frequency of IM1, IM2 and IM3 sequences in the whole genome was higher in GM-020 than in the other three Lactobacillus rhamnosus strains such as 4B15, DSM14870 and BPL5. It suggested that IM1, IM2, and IM3 sequences probably contribute to the specific functions of GM-020.







TABLE 1







the frequency of IM1, IM2 and IM3 sequences in the different strain of Lactobacillus rhamnosus
















GM-020
4B15
DSM 148709
BPL5


Code
Sequence
Genome size (bp)
3,037,161
3,047,840
3,013,150
3,024,030
















IM1
TTAGGG
Frequency
363
229
233
230




No. copies per 106 bases
11.96
7.51
7.73
7.60


IM2
TTTCGTTT
Frequency
98
60
66
65




No. copies per 106 bases
3.23
1.97
2.19
2.14


IM3
TCAAGCTTGA
Frequency
5
3
3
3




No. copies per 106 bases
0.16
0.10
0.10
0.10









Furthermore, the function of ODN with IM3 core sequence was tested with adipocytes. The five ODN sequences were characteristic of IM3 core sequence (TCAAGCTTGA) (SEQ ID NO. 12), and distinct sequences forward of 5′ TCAAGCTTGA and backward of TCAAGCTTGA 3′, named for IM3-1, IM3-2, IM3-3, IM3-4 and IM3-5, in Table 2.







TABLE 2







The five ODN sequences of GM-020 containing 


IM3 core sequence










Code
Core

ODN sequences of


name
sequence
SequenceID
GM-020





IM3
TCAAGCTTGA




 


IM3-1

SEQ ID NO. 1
CCATTTTCAAGCTTGACTTT


 


IM3-2

SEQ ID NO. 2
GACATTTCAAGCTTGAACAA


 


IM3-3

SEQ ID NO. 3
TTGGTGTCAAGCTTGACATC


 


IM3-4

SEQ ID NO. 4
TCAGGCTCAAGCTTGAGTTC


 


IM3-5

SEQ ID NO. 5
TAGGACTCAAGCTTGATCTC









Embodiment 2, Syntheses of CpG-ODN and Pretreatment
Five ODN fragments, IM3-1, IM3-2, IM3-3, IM3-4 and IM3-5, chemically synthesized by Genomics BioSci & Tech Co., Ltd., were based on the location of TCAAGCTTGA (SEQ ID NO. 12), five nucleotide bases forward of 5′ TCAAGCTTGA, and four nucleotide bases backward of TCAAGCTTGA3′ in the GM-020 genome. After being rapidly centrifuged, the powdered form of synthesized DNA was diluted to 200 μM with sodium chloride. After 10 minutes, the solutions were continuously diluted and prepared to be stock solutions with concentrations of 100, 50, 25 and 12.5 μM, respectively.
Embodiment 3, Cultivation of Adipocytes
Preadipocyte 3T3-L1 was seeded in DMEM medium with 10% FBS for two days and occupied to be 70% confluent. Then, cell culture medium was replaced by induction medium (10% FBS DMEM+1 μM Dexamethasone, 0.5 mM 3-isobutyl-1-methyl-xathine (IBMX) and 10 μg/mL insulin) and further by growth medium (10% FBS DMEM+10 μg/mL insulin) two days later. The cells were stimulated with IM3-1, -2, -3, -4 and -5. The growth medium (10% FBS DMEM+10 μg/mL insulin) containing IM3-1, -2, -3, -4 and -5 were replaced every three days until the end of experiment.
Embodiment 4, Lipogenesis Test
The adipocytes 3T3-L1 differentiated were flushed twice with PBS. The adipocytes were immobilized with 4% paraformaldehyde (PFA) at room temperate for 0.5 to 1 hour and flushed twice with pure water. Then, 60% isopropanol was added to the adipocytes for five minutes and then absorbed. The adipocytes were stained with Oil Red O for 10 to 20 minutes and were flushed twice with pure water until no stain color observed. The adipocytes were dipped with 60% isopropanol for five minutes. Lipid droplets inside adipocytes were dissolved out by 250 μL of 100% isopropanol. Finally, 200 μL of lipid droplets were carried on a 96-well plate for measurement of the optical density (OD) at the wave length 492 nm.
The differentiated adipocytes 3T3-L1 were stimulated with chemically synthesized IM3-1, -2, -3, -4, and -5, respectively. The intracellular lipid droplets were stained with Oil red O dyes and quantified based on the OD value. As shown in FIG. 2A and FIG. 2B, generation of lipid droplets in adipocytes were inhibited effectively when cells were stimulated with IM3-1 and IM3-5. In FIG. 3, IM3-2, IM3-3 and IM3-4 showed no effect on the inhibition of lipogenesis.
Embodiment 5, Expression of the FAS Gene (Lipogenesis-Related Gene)
RNA from adipocytes 3T3-L1 was extracted by TRIZol and to be a template transcribed to cDNA by Q-PCR mechine. Each reaction reagent contained 5 μL 2× Rotor-Gene SYBR Green PCR Master Mix (QIAGEN) in which 2 μL cDNA and 2 μL of 10 μM Forward (F)+Reverse (R) primers were added in turn. Primer sequences of FAS gene were (1) forward: GGAGGTGGTGATAGCCGGTAT (SEQ ID NO:6); (2) reversed: TGGGTAATCCATAGAGCCCAG (SEQ ID NO:7). Primer sequences of GAPDH gene were (1) forward: TGCACCACCAACTGCTTAGC (SEQ ID NO:8); (2) reversed: GGCATGGACTGTGGTCATGAG (SEQ ID NO:9). The reaction solution was placed inside the Q-PCR machine (model: QIAGEN Rotor-Gene Q 2Plex) for Real-time PCR (Real-time Pmerase Chain Reaction). After the house-keeping gene, GAPDH, and the amount of the relative expression for the control group, (2−ΔΔCt), were deducted from CT derived at Q-PCR in turn, the amount of gene expression was determined.







TABLE 3







The sequences of forward and reversed 


primer for FAS and GAPDH gene










Sequence 



Primer name
ID No.
Nucleotide sequence





Forward primer 
SEQ ID 
GGAGGTGGTGATAGCCGGTAT


of FAS gene
NO: 6



 


Reverse primer 
SEQ ID 
TGGGTAATCCATAGAGCCCAG


of FAS gene
NO: 7



 


Forward primer 
SEQ ID 
TGCACCACCAACTGCTTAGC


of GAPDH gene
NO: 8



 


Reverse primer 
SEQ ID 
GGCATGGACTGTGGTCATGAG


of GAPDH gene
NO: 9









Lipogenesis-related gene, such as FAS (fatty acid synthase), was over-expressed in the cells which accumulated lipids excessively. Therefore, FAS gene expression was further checked after adipocytes were simulated with IM3-1 or IM3-5. By the analysis of RT-PCR, the activation of FAS gene expressing was inhibited after adipocytes were simulated with IM3-1 or IM3-5 (FIG. 4). It can be seen from the present disclosure that two ODN sequences from GM-020 genome, IM3-1 (CCATTTTCAAGCTTGACTTT) (SEQ ID NO. 1) and IM3-5 (TAGGACTCAAGCTTGATCTC) (SEQ ID NO. 5), significantly inhibited lipid generation through down-regulating the lipogenesis-related gene expression, such as FAS.
The core sequence, TCAAGCTTGA (SEQ ID NO: 12), was unexceptionally contained in the five ODN fragments However, the sequence connecting with 5′ and 3′ ends of TCAAGCTTGA was distinct among the fragments. The results showed that the five ODN fragments had varying effect on the inhibition of lipogenesis. Only IM3-1 or IM3-5 exhibited a significant effect on lipogenesis inhibition, while IM3-2, IM3-3 or IM3-4 did not demonstrate the significant effect on lipogenesis inhibiting. In the present invention, through experimental measures such as the lipogenesis test and lipogenesis-related FAS gene expression, ODN fragments with health benefits provide a novel and safe prevention and improvement strategy for improving obesity caused by high-fat diet.
As disclosed in preferred embodiments of the patent specification, the embodiments are only examples well known to persons skilled in the art and having common knowledge. Any change or modification of the technical features in the patent specification made by persons skilled in the art and having common knowledge should not be taken as differences from the features in the present disclosure. The present invention could be fulfilled based on embodiments in the patent specification and even other changes in embodiments. As defined in claims of the patent specification, the scope of the present invention should cover the method as well as architecture mentioned above and any equivalent modification.
As presented in many effects hereinbefore, an application based on nucleotides of Lactobacillus rhamnosus to prepare a composition for anti-lipogenesis in the patent specification meets novelty and non-obviousness for patentability.
The above detailed descriptions are feasible embodiments of an application based on nucleotides of Lactobacillus rhamnosus to prepare a composition for anti-lipogenesis that should not restrict the scope of the present application. Any equivalent implementation or modification without departing from the spirit and scope of the present application should be incorporated in claims hereinafter.
Accordingly, it is to be understood that the embodiments of the invention herein described are merely illustrative of the application of the principles of the invention. Reference herein to details of the illustrated embodiments is not intended to limit the scope of the claims, which themselves recite those features regarded as essential to the invention.
As presented in many effects hereinbefore, an application based on nucleotides of Lactobacillus rhamnosus to prepare a composition for anti-lipogenesis in the patent specification meets novelty and non-obviousness for patentability.
Biological Material Deposit
Lactobacillus rhamnosus (also known as Lacticaseibacillus rhamnosus) GM-020 was deposited on Dec. 18, 2003 and has designation number CCTCC M203098 at the China Center for Type Culture Collection (CCTCC).