A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements
Background Alkanes are important components of fossil energy, such as crude oil. The alkane monooxygenase encoded by alkB gene performs the initial step of alkane degradation under aerobic conditions. The alkB gene is well studied due to its ubiquity as well as the availability of experimentally fun...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2022-09-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/14147.pdf |
| _version_ | 1797425651792216064 |
|---|---|
| author | Shaojing Wang Guoqiang Li Zitong Liao Tongtong Liu Ting Ma |
| author_facet | Shaojing Wang Guoqiang Li Zitong Liao Tongtong Liu Ting Ma |
| author_sort | Shaojing Wang |
| collection | DOAJ |
| description | Background Alkanes are important components of fossil energy, such as crude oil. The alkane monooxygenase encoded by alkB gene performs the initial step of alkane degradation under aerobic conditions. The alkB gene is well studied due to its ubiquity as well as the availability of experimentally functional evidence. The alkBFGHJKL and alkST clusters are special kind of alkB-type alkane hydroxylase system, which encode all proteins necessary for converting alkanes into corresponding fatty acids. Methods To explore whether the alkBFGHJKL and alkST clusters were widely distributed, we performed a large-scale analysis of isolate and metagenome assembled genome data (>390,000 genomes) to identify these clusters, together with distributions of corresponding taxonomy and niches. The set of alk-genes (including but not limited to alkBGHJ) located near each other on a DNA sequence was defined as an alk-gene cluster in this study. The alkB genes with alkGHJ located nearby on a DNA sequence were picked up for the investigation of putative alk-clusters. Results A total of 120 alk-gene clusters were found in 117 genomes. All the 117 genomes are from strains located only in α- and γ-proteobacteria. The alkB genes located in alk-gene sets were clustered into a deeply branched mono-clade. Further analysis showed similarity organization types of alk-genes were observed within closely related species. Although a large number of IS elements were observed nearby, they did not lead to the wide spread of the alk-gene cluster. The uneven distribution of these elements indicated that there might be other factors affecting the transmission of alk-gene clusters. Conclusions We conducted systematic bioinformatics research on alk-genes located near each other on a DNA sequence. This benchmark dataset of alk-genes can provide base line for exploring its evolutional and ecological importance in future studies. |
| first_indexed | 2024-03-09T08:19:10Z |
| format | Article |
| id | doaj.art-fffb5baf1b7749caaf2383f0e9f69bf3 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:19:10Z |
| publishDate | 2022-09-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-fffb5baf1b7749caaf2383f0e9f69bf32023-12-02T21:55:27ZengPeerJ Inc.PeerJ2167-83592022-09-0110e1414710.7717/peerj.14147A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elementsShaojing Wang0Guoqiang Li1Zitong Liao2Tongtong Liu3Ting Ma4College of Life Sciences, Nankai University, Tianjin, ChinaCollege of Life Sciences, Nankai University, Tianjin, ChinaCollege of Life Sciences, Nankai University, Tianjin, ChinaCollege of Life Sciences, Nankai University, Tianjin, ChinaCollege of Life Sciences, Nankai University, Tianjin, ChinaBackground Alkanes are important components of fossil energy, such as crude oil. The alkane monooxygenase encoded by alkB gene performs the initial step of alkane degradation under aerobic conditions. The alkB gene is well studied due to its ubiquity as well as the availability of experimentally functional evidence. The alkBFGHJKL and alkST clusters are special kind of alkB-type alkane hydroxylase system, which encode all proteins necessary for converting alkanes into corresponding fatty acids. Methods To explore whether the alkBFGHJKL and alkST clusters were widely distributed, we performed a large-scale analysis of isolate and metagenome assembled genome data (>390,000 genomes) to identify these clusters, together with distributions of corresponding taxonomy and niches. The set of alk-genes (including but not limited to alkBGHJ) located near each other on a DNA sequence was defined as an alk-gene cluster in this study. The alkB genes with alkGHJ located nearby on a DNA sequence were picked up for the investigation of putative alk-clusters. Results A total of 120 alk-gene clusters were found in 117 genomes. All the 117 genomes are from strains located only in α- and γ-proteobacteria. The alkB genes located in alk-gene sets were clustered into a deeply branched mono-clade. Further analysis showed similarity organization types of alk-genes were observed within closely related species. Although a large number of IS elements were observed nearby, they did not lead to the wide spread of the alk-gene cluster. The uneven distribution of these elements indicated that there might be other factors affecting the transmission of alk-gene clusters. Conclusions We conducted systematic bioinformatics research on alk-genes located near each other on a DNA sequence. This benchmark dataset of alk-genes can provide base line for exploring its evolutional and ecological importance in future studies.https://peerj.com/articles/14147.pdfAlkane monooxygenasealkBalk-gene clustersPhylogenetic diversityIS elementsNiches distribution |
| spellingShingle | Shaojing Wang Guoqiang Li Zitong Liao Tongtong Liu Ting Ma A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements PeerJ Alkane monooxygenase alkB alk-gene clusters Phylogenetic diversity IS elements Niches distribution |
| title | A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements |
| title_full | A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements |
| title_fullStr | A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements |
| title_full_unstemmed | A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements |
| title_short | A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements |
| title_sort | novel alkane monooxygenase alkb clade revealed by massive genomic survey and its dissemination association with is elements |
| topic | Alkane monooxygenase alkB alk-gene clusters Phylogenetic diversity IS elements Niches distribution |
| url | https://peerj.com/articles/14147.pdf |
| work_keys_str_mv | AT shaojingwang anovelalkanemonooxygenasealkbcladerevealedbymassivegenomicsurveyanditsdisseminationassociationwithiselements AT guoqiangli anovelalkanemonooxygenasealkbcladerevealedbymassivegenomicsurveyanditsdisseminationassociationwithiselements AT zitongliao anovelalkanemonooxygenasealkbcladerevealedbymassivegenomicsurveyanditsdisseminationassociationwithiselements AT tongtongliu anovelalkanemonooxygenasealkbcladerevealedbymassivegenomicsurveyanditsdisseminationassociationwithiselements AT tingma anovelalkanemonooxygenasealkbcladerevealedbymassivegenomicsurveyanditsdisseminationassociationwithiselements AT shaojingwang novelalkanemonooxygenasealkbcladerevealedbymassivegenomicsurveyanditsdisseminationassociationwithiselements AT guoqiangli novelalkanemonooxygenasealkbcladerevealedbymassivegenomicsurveyanditsdisseminationassociationwithiselements AT zitongliao novelalkanemonooxygenasealkbcladerevealedbymassivegenomicsurveyanditsdisseminationassociationwithiselements AT tongtongliu novelalkanemonooxygenasealkbcladerevealedbymassivegenomicsurveyanditsdisseminationassociationwithiselements AT tingma novelalkanemonooxygenasealkbcladerevealedbymassivegenomicsurveyanditsdisseminationassociationwithiselements |