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从烃污染土壤宏基因组中回收的未培养 Paracoccus sp. 的 ABC 转运蛋白和转座元件的功能特征。

Functional characterization of the ABC transporters and transposable elements of an uncultured Paracoccus sp. recovered from a hydrocarbon-polluted soil metagenome.

机构信息

Department of Biological Sciences, Microbiology Unit, Elizade University, Ilara-Mokin, Ondo State, Nigeria.

Department of Microbiology, Lagos State University, Ojo, Lagos, Nigeria.

出版信息

Folia Microbiol (Praha). 2023 Apr;68(2):299-314. doi: 10.1007/s12223-022-01012-0. Epub 2022 Nov 3.


DOI:10.1007/s12223-022-01012-0
PMID:36329216
Abstract

Environmental microorganisms usually exhibit a high level of genomic plasticity and metabolic versatility that allow them to be well-adapted to diverse environmental challenges. This study used shotgun metagenomics to decipher the functional and metabolic attributes of an uncultured Paracoccus recovered from a polluted soil metagenome and determine whether the detected attributes are influenced by the nature of the polluted soil. Functional and metabolic attributes of the uncultured Paracoccus were elucidated via functional annotation of the open reading frames (ORFs) of its contig. Functional tools deployed for the analysis include KEGG, KEGG KofamKOALA, Clusters of Orthologous Groups of proteins (COG), Comprehensive Antibiotic Resistance Database (CARD), and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT V6) for antibiotic resistance genes, TnCentral for transposable element, Transporter Classification Database (TCDB) for transporter genes, and FunRich for gene enrichment analysis. Analyses revealed the preponderance of ABC transporter genes responsible for the transport of oligosaccharides (malK, msmX, msmK, lacK, smoK, aglK, togA, thuK, treV, msiK), monosaccharides (glcV, malK, rbsC, rbsA, araG, ytfR, mglA), amino acids (thiQ, ynjD, thiZ, glnQ, gluA, gltL, peb1C, artP, aotP, bgtA, artQ, artR), and several others. Also detected are transporter genes for inorganic/organic nutrients like phosphate/phosphonate, nitrate/nitrite/cyanate, sulfate/sulfonate, bicarbonate, and heavy metals such as nickel/cobalt, molybdate/tungstate, and iron, among others. Antibiotic resistance genes that mediate efflux, inactivation, and target protection were detected, while transposable elements carrying resistance phenotypes for antibiotics and heavy metals were also annotated. The findings from this study have established the resilience, adaptability, and survivability of the uncultured Paracoccus in the hydrocarbon-polluted soil.

摘要

环境微生物通常表现出高水平的基因组可塑性和代谢多样性,这使它们能够很好地适应各种环境挑战。本研究使用鸟枪法宏基因组学来破译从污染土壤宏基因组中回收的未培养 Paracoccus 的功能和代谢属性,并确定检测到的属性是否受污染土壤性质的影响。通过对其基因组序列的开放阅读框(ORF)进行功能注释,阐明了未培养 Paracoccus 的功能和代谢属性。用于分析的功能工具包括 KEGG、KEGG KofamKOALA、蛋白质直系同源群(COG)、综合抗生素耐药数据库(CARD)和抗生素耐药基因-注释(ARG-ANNOT V6)用于抗生素耐药基因、TnCentral 用于转座元件、转运蛋白分类数据库(TCDB)用于转运蛋白基因和 FunRich 用于基因富集分析。分析表明,大量 ABC 转运蛋白基因负责寡糖(malK、msmX、msmK、lacK、smoK、aglK、togA、thuK、treV、msiK)、单糖(glcV、malK、rbsC、rbsA、araG、ytfR、mglA)、氨基酸(thiQ、ynjD、thiZ、glnQ、gluA、gltL、peb1C、artP、aotP、bgtA、artQ、artR)和其他几种物质的运输。还检测到无机/有机养分如磷酸盐/膦酸盐、硝酸盐/亚硝酸盐/氰酸盐、硫酸盐/磺酸盐、重碳酸盐和重金属如镍/钴、钼酸盐/钨酸盐和铁等的转运蛋白基因。检测到介导外排、失活和靶标保护的抗生素耐药基因,同时还注释了携带抗生素和重金属耐药表型的转座元件。本研究的结果确立了未培养 Paracoccus 在烃污染土壤中的弹性、适应性和生存能力。

相似文献

[1]
Functional characterization of the ABC transporters and transposable elements of an uncultured Paracoccus sp. recovered from a hydrocarbon-polluted soil metagenome.

Folia Microbiol (Praha). 2023-4

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[7]
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[8]
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[10]
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引用本文的文献

[1]
Transcriptome of TYL-A1 Revealed the Biotransformation Mechanism of Tylosin.

Microorganisms. 2024-12-16

[2]
Genome-resolved analysis of Serratia marcescens strain SMTT infers niche specialization as a hydrocarbon-degrader.

DNA Res. 2024-12-27

[3]
Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review.

Microorganisms. 2024-4-3

[4]
Identification and expression analysis of ATP-binding cassette (ABC) transporters revealed its role in regulating stress response in pear (Pyrus bretchneideri).

BMC Genomics. 2024-2-12

[5]
KEGG_Extractor: An Effective Extraction Tool for KEGG Orthologs.

Genes (Basel). 2023-2-1

本文引用的文献

[1]
Harnessing taxonomically diverse and metabolically versatile genus Paracoccus for bioplastic synthesis and xenobiotic biodegradation.

J Appl Microbiol. 2022-6

[2]
Amino Acids in Microbial Metabolism and Function.

Adv Exp Med Biol. 2022

[3]
Impact of spent engine oil contamination on the antibiotic resistome of a tropical agricultural soil.

Ecotoxicology. 2021-8

[4]
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.

Nucleic Acids Res. 2021-1-8

[5]
The novel macrolide resistance genes mef(F) and msr(G) are located on a plasmid in Macrococcus canis and a transposon in Macrococcus caseolyticus.

J Antimicrob Chemother. 2021-1-1

[6]
Target protection as a key antibiotic resistance mechanism.

Nat Rev Microbiol. 2020-11

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Management of Osmoprotectant Uptake Hierarchy in via a SigB-Dependent Antisense RNA.

Front Microbiol. 2020-4-21

[8]
The Novel Macrolide Resistance Genes (D), (F), and (H) Are Present on Resistance Islands in Macrococcus canis, Macrococcus caseolyticus, and Staphylococcus aureus.

Antimicrob Agents Chemother. 2020-4-21

[9]
A potassium chloride to glycine betaine osmoprotectant switch in the extreme halophile Halorhodospira halophila.

Sci Rep. 2020-2-25

[10]
Complete genome sequence of Paracoccus sp. strain AK26: Insights into multipartite genome architecture and methylotropy.

Genomics. 2020-5

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