Draft genome sequencing of Sporolactobacillus terrae SBT-1, an efficient bacterium to ferment concentrated sugar to d-lactic acid

Thitiprasert, Sitanan; Piluk, Jirabhorn; Tolieng, Vasana; Tanaka, Naoto; Shiwa, Yuh; Fujita, Nobuyuki; Tanasupawat, Somboon; Thongchul, Nuttha

doi:10.1007/s00203-021-02352-0

Cited by 9 publications

(7 citation statements)

References 32 publications

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“…Two whole-genome-based methods were used to construct phylogenetic trees. The first phylogenetic tree was constructed with the CV method using the whole amino acid sequences of forty-one B. cereus group strains and the outgroup species T. sporolactobacillus [32]. To ensure the accuracy of the results, we added the inbuilt sequence AH1273 and the sequence of T. sporolactobacillus (control) from the webserver database (Fig 1).…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic and protein prediction analysis reveals the taxonomically diverse distribution of virulence factors in the Bacillus cereus group

Zhang

Yin

et al. 2022

Preprint

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Bacillus cereus is a food contaminant with widely varying enterotoxic potential of its virulence proteins. In this article, phylogenetic analysis of the whole-genome amino acid sequences of 41 strains, evolutionary distance calculation of the amino acid sequences of the virulence genes, and functional and structural prediction of the virulence proteins were performed to reveal the taxonomically diverse distribution of virulence factors. The genome evolution of the strains showed a clustering trend based on the coding virulence genes. The strains of B. cereus have evolved into non-toxic risk and toxic risk clusters with medium-high- and medium-low-risk clusters. The distances of evolutionary transfer relative to housekeeping genes of incomplete virulence genes were greater than those of complete virulence genes, and the distance values of HblACD were higher than those of nheABC and CytK among the complete virulence genes. Cytoplasmic localization was impossible for all the virulence proteins, and NheB, NheC, Hbl-B, and Hbl-L 1 were extracellular according to predictive analysis. Nhe and Hbl proteins except CytK had similar spatial structures. The predicted structures of Nhe and Hbl mainly showed ‘head’ and ‘tail’ domains. The ‘head’ of NheA and Hbl-B, including two α-helices separated by β-tongue strands, might play a special role in Nhe trimers and Hbl trimers, respectively. The ‘cap’ of CytK, which includes two ‘latches’ with many β-sheets, formed a β-barrel structure with pores, and a ‘rim’ balanced the structure. The evolution of B. cereus strains showed a clustering tendency based on the coding virulence genes, and the complete virulence-gene operon combination had higher relative genetic stability. The beta-tongue or latch associated with β-sheet folding might play an important role in the binding of virulence structures and pore-forming toxins in B. cereus .

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Section: Resultsmentioning

confidence: 99%

Phylogenetic and protein prediction analysis reveals the taxonomically diverse distribution of virulence factors in the Bacillus cereus group

Zhang

Yin

et al. 2022

Preprint

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“…cereus strains and the outgroup species S . terrae 70–3 [ 35 ]. To ensure the accuracy of the results, we added the inbuilt sequence AH1273 and the sequence of S .…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic and protein prediction analysis reveals the taxonomically diverse distribution of virulence factors in Bacillus cereus strains

Zhang

Yin

et al. 2022

PLoS ONE

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Bacillus cereus is a food contaminant with widely varying enterotoxic potential due to its virulence proteins. In this article, phylogenetic analysis of the amino acid sequences from the whole-genomes of 41 strains, evolutionary distance calculation of the amino acid sequences of the virulence genes, and functional and structural predictions of the virulence proteins were performed to reveal the taxonomically diverse distribution of virulence factors. The genome evolution of the strains showed a clustering trend based on the protein-coding virulence genes. The strains of B. cereus have evolved into non-toxic risk and toxic risk clusters with medium-high- and medium-low-risk subclusters. The evolutionary transfer distances of incomplete virulence genes relative to housekeeping genes were greater than those of complete virulence genes, and the distance values of HblACD were higher than those of nheABC and CytK among the complete virulence genes. Cytoplasmic localization was impossible for all the virulence proteins, and NheB, NheC, Hbl-B, and Hbl-L1 were predicted to be extracellular. Nhe and Hbl proteins except CytK had similar spatial structures. The predicted structures of Nhe and Hbl mainly showed ‘head’ and ‘tail’ domains. The ‘head’ of NheA and Hbl-B, including two α-helices separated by β-tongue strands, might play a special role in the formation of Nhe trimers and Hbl trimers, respectively. The ‘cap’ of CytK, which includes two ‘latches’ with many β-sheets, formed a β-barrel structure with pores, and a ‘rim’ balanced the structure. The evolution of B. cereus strains showed a clustering tendency based on the protein-coding virulence genes, and the complete virulence-gene operon combination had higher relative genetic stability. The beta-tongue or latch associated with β-sheet folding might play an important role in the binding of virulence structures and pore-forming toxins in B. cereus.

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“…S. terrae SBT-1 from our laboratory collection was used to evaluate enzymatic reaction, gene transcription, and d -lactic acid production. This bacterial strain exhibits superior activity in the fermentation of glucose or sucrose at extremely high concentrations into d -lactic acid 13 . A stock culture of S. terrae SBT-1 was maintained in 10% (w/v) skimmed milk and stored at − 80 °C.…”

Section: Methodsmentioning

confidence: 99%

“…In our previous study, we reported the efficiency of the new isolate S. terrae SBT-1 for producing high d -lactic acid (up to 290 g/L) under high sugar concentration (up to 440 g/L). Three potential D-LDH-, two L-LDH-encoding genes ( ldh Ds and ldh Ls), as well as a lactate racemase-encoding gene ( lar A) which involved in optically pure lactic acid isomers were annotated from the whole-genome sequence of SBT-1 13 . However, it was noticed that enantiomeric ratio of d -lactic acid was influenced when varying fermentation substrates.…”

Section: Introductionmentioning

confidence: 99%

Association between organic nitrogen substrates and the optical purity of d-lactic acid during the fermentation by Sporolactobacillus terrae SBT-1

Thitiprasert,

Jaiaue,

Amornbunchai

et al. 2024

Sci Rep

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The development of biotechnological lactic acid production has attracted attention to the potential production of an optically pure isomer of lactic acid, although the relationship between fermentation and the biosynthesis of highly optically pure d-lactic acid remains poorly understood. Sporolactobacillus terrae SBT-1 is an excellent d-lactic acid producer that depends on cultivation conditions. Herein, three enzymes responsible for synthesizing optically pure d-lactic acid, including d-lactate dehydrogenase (D-LDH; encoded by ldhDs), l-lactate dehydrogenase (L-LDH; encoded by ldhLs), and lactate racemase (Lar; encoded by larA), were quantified under different organic nitrogen sources and concentration to study the relationship between fermentation conditions and synthesis pathway of optically pure lactic acid. Different organic nitrogen sources and concentrations significantly affected the quantity and quality of d-lactic acid produced by strain SBT-1 as well as the synthetic optically pure lactic acid pathway. Yeast extract is a preferred organic nitrogen source for achieving high catalytic efficiency of d-lactate dehydrogenase and increasing the transcription level of ldhA2, indicating that this enzyme plays a major role in d-lactic acid formation in S. terrae SBT-1. Furthermore, lactate racemization activity could be regulated by the presence of d-lactic acid. The results of this study suggest that specific nutrient requirements are necessary to achieve a stable and highly productive fermentation process for the d-lactic acid of an individual strain.

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Draft genome sequencing of Sporolactobacillus terrae SBT-1, an efficient bacterium to ferment concentrated sugar to d-lactic acid

Cited by 9 publications

References 32 publications

Phylogenetic and protein prediction analysis reveals the taxonomically diverse distribution of virulence factors in the Bacillus cereus group

Phylogenetic and protein prediction analysis reveals the taxonomically diverse distribution of virulence factors in the Bacillus cereus group

Phylogenetic and protein prediction analysis reveals the taxonomically diverse distribution of virulence factors in Bacillus cereus strains

Association between organic nitrogen substrates and the optical purity of d-lactic acid during the fermentation by Sporolactobacillus terrae SBT-1

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