Comparative genome analysis of four Leuconostoc strains with a focus on carbohydrate-active enzymes and oligosaccharide utilization pathways
Leuconostoc is mostly found in food, plants, and dairy products. Due to their innate genomic features, such as the presence of carbohydrate-active enzymes, bacteriocins, and plasmids, Leuconostoc spp. have great biotechnological potential. In this study, four strains were isolated and identified as...
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S200103702200366X |
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| author | Anshul Sharma Neha Sharma Deepshikha Gupta Hae-Jeung Lee Young-Seo Park |
| author_facet | Anshul Sharma Neha Sharma Deepshikha Gupta Hae-Jeung Lee Young-Seo Park |
| author_sort | Anshul Sharma |
| collection | DOAJ |
| description | Leuconostoc is mostly found in food, plants, and dairy products. Due to their innate genomic features, such as the presence of carbohydrate-active enzymes, bacteriocins, and plasmids, Leuconostoc spp. have great biotechnological potential. In this study, four strains were isolated and identified as Leuconostoc mesenteroides SG315 (LA), L. citreum SG255 (LB), L. lactis CCK940 (LC), and L. lactis SBC001 (LD). Comparative analysis was performed using their draft genome sequences. Differences among the four strains were analyzed using the average nucleotide identity, dot plot, and multiple alignments of conserved genomic sequences. Functional profiling revealed 2134, 1917, 1751, and 1816 open reading frames; 2023, 1823, 1655, and 1699 protein-coding genes; 60, 57, 83, and 82 RNA-coding genes; and GC content of 37.5 %, 38.8 %, 43.3 %, and 43.2 %, in LA, LB, LC, and LD, respectively. The total number of genes encoding carbohydrate-active enzymes was 76 (LA), 73 (LB), 57 (LC), and 67 (LD). These results indicate that the four strains shared a large number of genes, but their gene content is different. Furthermore, most genes with unknown functions were observed in the prophage regions of the genome. This study also elucidated the oligosaccharide utilization and folate biosynthesis pathways in Leuconostoc spp. Taken together, our findings provide useful information on the genomic diversity of CAZymes in the four Leuconostoc strains and suggest that these species could be used for potent exploitation. |
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| format | Article |
| id | doaj.art-256f67e53b1b433f913c56c815739822 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:19:14Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
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| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-256f67e53b1b433f913c56c8157398222022-12-24T04:54:00ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012047714785Comparative genome analysis of four Leuconostoc strains with a focus on carbohydrate-active enzymes and oligosaccharide utilization pathwaysAnshul Sharma0Neha Sharma1Deepshikha Gupta2Hae-Jeung Lee3Young-Seo Park4Department of Food and Nutrition, Gachon University, Seongnam-si 13120, Gyeonggi-do, South KoreaDepartment of Food Science and Biotechnology, Gachon University, Seongnam-si 13120, Gyeonggi-do, South KoreaDepartment of Plant Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India; DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, Telangana, IndiaDepartment of Food and Nutrition, Gachon University, Seongnam-si 13120, Gyeonggi-do, South Korea; Institute for Aging and Clinical Nutrition Research, Gachon University, Seongnam-si 13120, Gyeonggi-do, South KoreaDepartment of Food Science and Biotechnology, Gachon University, Seongnam-si 13120, Gyeonggi-do, South Korea; Corresponding author.Leuconostoc is mostly found in food, plants, and dairy products. Due to their innate genomic features, such as the presence of carbohydrate-active enzymes, bacteriocins, and plasmids, Leuconostoc spp. have great biotechnological potential. In this study, four strains were isolated and identified as Leuconostoc mesenteroides SG315 (LA), L. citreum SG255 (LB), L. lactis CCK940 (LC), and L. lactis SBC001 (LD). Comparative analysis was performed using their draft genome sequences. Differences among the four strains were analyzed using the average nucleotide identity, dot plot, and multiple alignments of conserved genomic sequences. Functional profiling revealed 2134, 1917, 1751, and 1816 open reading frames; 2023, 1823, 1655, and 1699 protein-coding genes; 60, 57, 83, and 82 RNA-coding genes; and GC content of 37.5 %, 38.8 %, 43.3 %, and 43.2 %, in LA, LB, LC, and LD, respectively. The total number of genes encoding carbohydrate-active enzymes was 76 (LA), 73 (LB), 57 (LC), and 67 (LD). These results indicate that the four strains shared a large number of genes, but their gene content is different. Furthermore, most genes with unknown functions were observed in the prophage regions of the genome. This study also elucidated the oligosaccharide utilization and folate biosynthesis pathways in Leuconostoc spp. Taken together, our findings provide useful information on the genomic diversity of CAZymes in the four Leuconostoc strains and suggest that these species could be used for potent exploitation.http://www.sciencedirect.com/science/article/pii/S200103702200366XLeuconostoc mesenteroidesLeuconostoc citreumLeuconostoc lactisComparative genomicsCarbohydrate-active enzymesOligosaccharide |
| spellingShingle | Anshul Sharma Neha Sharma Deepshikha Gupta Hae-Jeung Lee Young-Seo Park Comparative genome analysis of four Leuconostoc strains with a focus on carbohydrate-active enzymes and oligosaccharide utilization pathways Computational and Structural Biotechnology Journal Leuconostoc mesenteroides Leuconostoc citreum Leuconostoc lactis Comparative genomics Carbohydrate-active enzymes Oligosaccharide |
| title | Comparative genome analysis of four Leuconostoc strains with a focus on carbohydrate-active enzymes and oligosaccharide utilization pathways |
| title_full | Comparative genome analysis of four Leuconostoc strains with a focus on carbohydrate-active enzymes and oligosaccharide utilization pathways |
| title_fullStr | Comparative genome analysis of four Leuconostoc strains with a focus on carbohydrate-active enzymes and oligosaccharide utilization pathways |
| title_full_unstemmed | Comparative genome analysis of four Leuconostoc strains with a focus on carbohydrate-active enzymes and oligosaccharide utilization pathways |
| title_short | Comparative genome analysis of four Leuconostoc strains with a focus on carbohydrate-active enzymes and oligosaccharide utilization pathways |
| title_sort | comparative genome analysis of four leuconostoc strains with a focus on carbohydrate active enzymes and oligosaccharide utilization pathways |
| topic | Leuconostoc mesenteroides Leuconostoc citreum Leuconostoc lactis Comparative genomics Carbohydrate-active enzymes Oligosaccharide |
| url | http://www.sciencedirect.com/science/article/pii/S200103702200366X |
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