Reconstruction and analysis of the genome-scale metabolic model of Lactobacillus casei LC2W

Xu, Nan; Liu, Jie; Ai, Lianzhong; Li, Liming

doi:10.1016/j.gene.2014.10.034

Cited by 29 publications

(17 citation statements)

References 47 publications

(42 reference statements)

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“…The report of Wu and Shah (2018) also support this finding. Previous studies on L. paracasei LC2W ( Xu et al, 2015 ) and L. kefiranofaciens ZW3 ( Xing et al, 2017 ) indicated the absence of corresponding genes that lead to GDP-mannose production in these strains, suggesting that the mannose in its EPS might be derived from medium. From this study we understand that UDP-glucose and UDP-galactose should be the major nucleotide sugars involved in EPS production by S. thermophilus 1275 with traces of UDP- N -acetylglucosamine and UDP-galactofuranose.…”

Section: Discussionmentioning

confidence: 94%

Transcriptomic Insights Into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275

Padmanabhan

Tong

et al. 2018

Front. Microbiol.

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In a previous study, incorporation of high exopolysaccharide (EPS) producing dairy starter bacterium Streptococcus thermophilus ASCC 1275 was found to improve functionality of low fat mozzarella cheese and yogurt. This bacterium in its eps gene cluster has a unique pair of chain length determining genes, epsC- epsD, when compared to other sequenced S. thermophilus strains. Hence, the aim of this study was to understand the regulatory mechanism of EPS production in this bacterium using transcriptomic analysis to provide opportunities to improve the yield of EPS. As sugars are considered as one of the major determinants of EPS production, after preliminary screening, we selected three sugars, glucose, sucrose and lactose to identify the EPS producing mechanism of this bacterium in M17 medium. Complete RNA-seq analysis was performed using Illumina HiSeq 2000 sequencing system on S. thermophilus 1275 grown in three different sugars at two-time points, 5 h (log phase) and 10 h (stationary phase) to recognize the genes involved in sugar uptake, UDP-sugar formation, EPS assembly and export of EPS outside the bacterial cell. S. thermophilus 1275 was found to produce high amount of EPS (∼430 mg/L) in sucrose (1%) supplemented M17 medium when compared to other two sugars. Differential gene expression analysis revealed the involvement of phosphoenolpyruvate phosphotransferase system (PEP-PTS) for glucose and sucrose uptake, and lacS gene for lactose uptake. The pathways for the formation of UDP-glucose and UDP-galactose were highly upregulated in all the three sugars. In the presence of sucrose, eps1C1D2C2D were found to be highly expressed which refers to high EPS production. Protein homology study suggested the presence of Wzx/Wzy-dependent EPS synthesis and transport pathway in this bacterium. KEGG pathway and COG functional enrichment analysis were also performed to support the result. This is the first report providing the transcriptomic insights into the EPS production mechanism of a common dairy bacterium, S. thermophilus.

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Section: Discussionmentioning

confidence: 94%

Transcriptomic Insights Into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275

Padmanabhan

Tong

et al. 2018

Front. Microbiol.

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“…A previous report similarly indicated the lack of a corresponding enzyme system in Lb . paracasei LC2W, suggesting that the mannose component of its EPS may be derived from the medium, mannose-6-phosphate, or epoxidose 48 . Thus, we only investigated the catalytic fructose-6-phosphate to mannose-6-phosphate step mediated by mpi .…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics of Lactobacillus kefiranofaciens ZW3 and related members of Lactobacillus. spp reveal adaptations to dairy and gut environments

Xing

Geng

et al. 2017

Sci Rep

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It is important for probiotics that are currently utilized in the dairy industry to have clear genetic backgrounds. In this study, the genetic characteristics of Lactobacillus kefiranofaciens ZW3 were studied by undertaking a comparative genomics study, and key genes for adaptation to different environments were investigated and validated in vitro. Evidence for horizontal gene transfer resulting in strong self-defense mechanisms was detected in the ZW3 genome. We identified a series of genes relevant for dairy environments and the intestinal tract, particularly for extracellular polysaccharide (EPS) production. Reverse transcription-qPCR (RT-qPCR) revealed significant increases in the relative expression of pgm, ugp, and uge during the mid-logarithmic phase, whereas the expression of pgi was higher at the beginning of the stationary phase. The enzymes encoded by these four genes concertedly regulated carbon flux, which in turn modulated the production of EPS precursors. Moreover, ZW3 tolerated pH 3.5 and 3% bile salt and retained cell surface hydrophobicity and auto-aggregation. In conclusion, we explored the potential of ZW3 for utilization in both the dairy industry and in probiotic applications. Additionally, we elucidated the regulation of the relevant genes involved in EPS production.

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“…The availability of software applications to conveniently implement FBA and related in silico methods 20 has enabled the development of genome-scale models (GEMs) for more than 100 species across all three domains of life, thereby facilitating analysis of their intracellular metabolism 21 . However, with respect to LAB, only a handful of GEMs are available, including Lactococcus lactis 22 – 24 , Lactobacillus plantarum 25 , Streptococcus thermophilus 26 and Lactobacillus casei 27 , 28 although more than 100 LAB genomes have been sequenced 29 . Note that these species with available GEMs belong to either homolactic or facultatively heterolactic fermenting groups.…”

Section: Introductionmentioning

confidence: 99%

Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria

Koduru

Kim

Bang

et al. 2017

Sci Rep

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Obligate heterofermentative lactic acid bacteria (LAB) are well-known for their beneficial health effects in humans. To delineate the incompletely characterized metabolism that currently limits their exploitation, at systems-level, we developed a genome-scale metabolic model of the representative obligate heterofermenting LAB, Leuconostoc mesenteroides (iLME620). Constraint-based flux analysis was then used to simulate several qualitative and quantitative phenotypes of L. mesenteroides, thereby evaluating the model validity. With established predictive capabilities, we subsequently employed iLME620 to elucidate unique metabolic characteristics of L. mesenteroides, such as the limited ability to utilize amino acids as energy source, and to substantiate the role of malolactic fermentation (MLF) in the reduction of pH-homeostatic burden on F0F1-ATPase. We also reported new hypothesis on the MLF mechanism that could be explained via a substrate channelling-like phenomenon mainly influenced by intracellular redox state rather than the intermediary reactions. Model simulations further revealed possible proton-symporter dependent activity of the energy efficient glucose-phosphotransferase system in obligate heterofermentative LAB. Moreover, integrated transcriptomic analysis allowed us to hypothesize transcriptional regulatory bias affecting the intracellular redox state. The insights gained here about the low ATP-yielding metabolism of L. mesenteroides, dominantly controlled by the cellular redox state, could potentially aid strain design for probiotic and cell factory applications.

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Reconstruction and analysis of the genome-scale metabolic model of Lactobacillus casei LC2W

Cited by 29 publications

References 47 publications

Transcriptomic Insights Into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275

Transcriptomic Insights Into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275

Comparative genomics of Lactobacillus kefiranofaciens ZW3 and related members of Lactobacillus. spp reveal adaptations to dairy and gut environments

Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria

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