Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood–Ljungdahl pathway
Abstract Acetogenic bacteria are obligate anaerobes with the ability of converting carbon dioxide and other one‐carbon substrates into acetate through the Wood–Ljungdahl (WL) pathway. These substrates are becoming increasingly important feedstock in industrial microbiology. The main potential indust...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2019-12-01
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| Series: | MicrobiologyOpen |
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| Online Access: | https://doi.org/10.1002/mbo3.938 |
| _version_ | 1818853957659787264 |
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| author | Alfonso Esposito Sabrina Tamburini Luca Triboli Luca Ambrosino Maria Luisa Chiusano Olivier Jousson |
| author_facet | Alfonso Esposito Sabrina Tamburini Luca Triboli Luca Ambrosino Maria Luisa Chiusano Olivier Jousson |
| author_sort | Alfonso Esposito |
| collection | DOAJ |
| description | Abstract Acetogenic bacteria are obligate anaerobes with the ability of converting carbon dioxide and other one‐carbon substrates into acetate through the Wood–Ljungdahl (WL) pathway. These substrates are becoming increasingly important feedstock in industrial microbiology. The main potential industrial application of acetogenic bacteria is the production of metabolites that constitute renewable energy sources (biofuel); such bacteria are of particular interest for this purpose thanks to their low energy requirements for large‐scale cultivation. Here, we report new genome sequences for four species, three of them are reported for the first time, namely Acetobacterium paludosum DSM 8237, Acetobacterium tundrae DSM 917, Acetobacterium bakii DSM 8239, and Alkalibaculum bacchi DSM 221123. We performed a comparative genomic analysis focused on the WL pathway's genes and their encoded proteins, using Acetobacterium woodii as a reference genome. The Average Nucleotide Identity (ANI) values ranged from 70% to 95% over an alignment length of 5.4–6.5 Mbp. The core genome consisted of 363 genes, whereas the number of unique genes in a single genome ranged from 486 in A. tundrae to 2360 in A.bacchi. No significant rearrangements were detected in the gene order for the Wood–Ljungdahl pathway however, two species showed variations in genes involved in formate metabolism: A. paludosum harbor two copies of fhs1, and A. bakii a truncated fdhF1. The analysis of protein networks highlighted the expansion of protein orthologues in A. woodii compared to A. bacchi, whereas protein networks involved in the WL pathway were more conserved. This study has increased our understanding on the evolution of the WL pathway in acetogenic bacteria. |
| first_indexed | 2024-12-19T07:45:04Z |
| format | Article |
| id | doaj.art-c03905f66c5a4f409f183caddb19c284 |
| institution | Directory Open Access Journal |
| issn | 2045-8827 |
| language | English |
| last_indexed | 2024-12-19T07:45:04Z |
| publishDate | 2019-12-01 |
| publisher | Wiley |
| record_format | Article |
| series | MicrobiologyOpen |
| spelling | doaj.art-c03905f66c5a4f409f183caddb19c2842022-12-21T20:30:22ZengWileyMicrobiologyOpen2045-88272019-12-01812n/an/a10.1002/mbo3.938Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood–Ljungdahl pathwayAlfonso Esposito0Sabrina Tamburini1Luca Triboli2Luca Ambrosino3Maria Luisa Chiusano4Olivier Jousson5Department of Cellular, Computational and Integrative Biology—CIBIO University of Trento Trento ItalyDepartment of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai NY USADepartment of Cellular, Computational and Integrative Biology—CIBIO University of Trento Trento ItalyResearch Infrastructures for Marine Biological Resources (RIMAR) Stazione Zoologica Anton Dohrn Naples ItalyDepartment of Agricultural sciences University of Naples “Federico II” Portici ItalyDepartment of Cellular, Computational and Integrative Biology—CIBIO University of Trento Trento ItalyAbstract Acetogenic bacteria are obligate anaerobes with the ability of converting carbon dioxide and other one‐carbon substrates into acetate through the Wood–Ljungdahl (WL) pathway. These substrates are becoming increasingly important feedstock in industrial microbiology. The main potential industrial application of acetogenic bacteria is the production of metabolites that constitute renewable energy sources (biofuel); such bacteria are of particular interest for this purpose thanks to their low energy requirements for large‐scale cultivation. Here, we report new genome sequences for four species, three of them are reported for the first time, namely Acetobacterium paludosum DSM 8237, Acetobacterium tundrae DSM 917, Acetobacterium bakii DSM 8239, and Alkalibaculum bacchi DSM 221123. We performed a comparative genomic analysis focused on the WL pathway's genes and their encoded proteins, using Acetobacterium woodii as a reference genome. The Average Nucleotide Identity (ANI) values ranged from 70% to 95% over an alignment length of 5.4–6.5 Mbp. The core genome consisted of 363 genes, whereas the number of unique genes in a single genome ranged from 486 in A. tundrae to 2360 in A.bacchi. No significant rearrangements were detected in the gene order for the Wood–Ljungdahl pathway however, two species showed variations in genes involved in formate metabolism: A. paludosum harbor two copies of fhs1, and A. bakii a truncated fdhF1. The analysis of protein networks highlighted the expansion of protein orthologues in A. woodii compared to A. bacchi, whereas protein networks involved in the WL pathway were more conserved. This study has increased our understanding on the evolution of the WL pathway in acetogenic bacteria.https://doi.org/10.1002/mbo3.938AcetogensComparative genomicsNGSWood–Ljungdahl pathway |
| spellingShingle | Alfonso Esposito Sabrina Tamburini Luca Triboli Luca Ambrosino Maria Luisa Chiusano Olivier Jousson Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood–Ljungdahl pathway MicrobiologyOpen Acetogens Comparative genomics NGS Wood–Ljungdahl pathway |
| title | Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood–Ljungdahl pathway |
| title_full | Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood–Ljungdahl pathway |
| title_fullStr | Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood–Ljungdahl pathway |
| title_full_unstemmed | Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood–Ljungdahl pathway |
| title_short | Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood–Ljungdahl pathway |
| title_sort | insights into the genome structure of four acetogenic bacteria with specific reference to the wood ljungdahl pathway |
| topic | Acetogens Comparative genomics NGS Wood–Ljungdahl pathway |
| url | https://doi.org/10.1002/mbo3.938 |
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