A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements

Abstract

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.

Genome-Wide Expression Analysis Unravels Fluoroalkane Metabolism in Pseudomonas sp. Strain 273

“…Pseudomonas sp. strain RW407 was isolated from polluted sediment of the Elbe River in Germany, Pseudomonas citronellolis strain P3B5 was isolated from the basil plant phyllosphere, and strain 273 was obtained from garden soil collected in the Stuttgart area, Germany. , The high sequence similarity between alkB -2 of strain 273 and the alkB genes of strain RW407 and strain P3B5 could indicate horizontal gene transfer, an observation supported by a recent study that analyzed alkB genes in a genomic context and concluded that horizontal gene transfer events contribute substantially to the dissemination of alkB genes …”

“…18,59 The high sequence similarity between alkB-2 of strain 273 and the alkB genes of strain RW407 and strain P3B5 could indicate horizontal gene transfer, an observation supported by a recent study that analyzed alkB genes in a genomic context and concluded that horizontal gene transfer events contribute substantially to the dissemination of alkB genes. 61 The comparative transcriptome analysis revealed a unique AlkB alkane monooxygenase with a novel AlkB Fd-Rd architecture involved in the initial attack on decane and DFD. AlkB-2 is the first enzyme of this type implicated in oxygenolytic defluorination, offering opportunities to investigate features distinguishing AlkB enzymes that attack a terminal fluoromethyl group.…”

Isolation and screening of indigenous nitrifying bacteria to enhance nutrient recovery in an aquaponics system

“…Sofar, M. nauticus has been reported to have the capacity for pollution degradation. For instance, M. nauticus has been described to degrade an acyclic saturated hydrocarbon (alkane) under aerobic conditions due to its capacity to synthesize alkane monooxygenase (Wang et al, 2022). Another study reported that M. nauticus isolated from water of an oil field in Vietnam was able to grow in wide ranges of temperatures (13°C–50°C) and salinity (0–20% NaCl) (Huu et al, 1999), therefore consider as a halotolerant bacterium (Tourova et al, 2022).…”

Monitoreo de contaminantes y detección de genes alkb en la Zona Común de Pesca Argentino-Uruguaya

“…Los clusters de genes alkB codifican todas las proteínas necesarias para convertir los alcanos en los correspondientes ácidos grasos, dotando a los microorganismos con la habilidad de utilizar alcanos como única fuente de carbono y energía (Wang et al 2022). Usualmente, existe un gen por genoma, aunque en algunas especies se han hallado dos o más genes alkB redundantes (Whyte et al 2002).…”