Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the <italic toggle="yes">pmoCAB</italic> Operon of Type Ia Methanotrophs

ABSTRACT Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle and a sink for greenhouse gas. Microorganisms that oxidize methane (m...

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Autores principales:	Juan C. Villada, Maria F. Duran, Patrick K. H. Lee
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	codon usage methane monooxygenase resource allocation synthesis cost translation efficiency Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/64c1460ee1ab4024ad814955c2ee9a31
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spelling	oai:doaj.org-article:64c1460ee1ab4024ad814955c2ee9a312021-12-02T18:44:37ZGenomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the <italic toggle="yes">pmoCAB</italic> Operon of Type Ia Methanotrophs10.1128/mSystems.00342-192379-5077https://doaj.org/article/64c1460ee1ab4024ad814955c2ee9a312019-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00342-19https://doaj.org/toc/2379-5077ABSTRACT Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle and a sink for greenhouse gas. Microorganisms that oxidize methane (methanotrophs) are taxonomically diverse and widespread around the globe. In methanotrophic bacteria, enzymes in the methane oxidation metabolic module (KEGG module M00174, conversion of methane to formaldehyde) are encoded in four operons (pmoCAB, mmoXYZBCD, mxaFI, and xoxF). Recent reports have suggested that methanotrophs in Proteobacteria acquired methane monooxygenases through horizontal gene transfer. Here, we used a genomic meta-analysis to infer the transcriptional and translational advantages of coding sequences from the methane oxidation metabolic modules of different types of methanotrophs. By analyzing isolate and metagenome-assembled genomes from phylogenetically and geographically diverse sources, we detected an anomalous nucleotide composition bias in the coding sequences of particulate methane monooxygenase genes (pmoCAB) from type Ia methanotrophs. We found that this nucleotide bias increases the level of codon bias by decreasing the GC content in the third base of codons, a strategy that contrasts with that of other coding sequences in the module. Further codon usage analyses uncovered that codon variants of the type Ia pmoCAB coding sequences deviate from the genomic signature to match ribosomal protein-coding sequences. Subsequently, computation of transcription and translation metrics revealed that the pmoCAB coding sequences of type Ia methanotrophs optimize the usage of codon variants to maximize translation efficiency and accuracy, while minimizing the synthesis cost of transcripts and proteins. IMPORTANCE Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.Juan C. VilladaMaria F. DuranPatrick K. H. LeeAmerican Society for Microbiologyarticlecodon usagemethane monooxygenaseresource allocationsynthesis costtranslation efficiencyMicrobiologyQR1-502ENmSystems, Vol 4, Iss 4 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	codon usage methane monooxygenase resource allocation synthesis cost translation efficiency Microbiology QR1-502
spellingShingle	codon usage methane monooxygenase resource allocation synthesis cost translation efficiency Microbiology QR1-502 Juan C. Villada Maria F. Duran Patrick K. H. Lee Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the <italic toggle="yes">pmoCAB</italic> Operon of Type Ia Methanotrophs
description	ABSTRACT Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle and a sink for greenhouse gas. Microorganisms that oxidize methane (methanotrophs) are taxonomically diverse and widespread around the globe. In methanotrophic bacteria, enzymes in the methane oxidation metabolic module (KEGG module M00174, conversion of methane to formaldehyde) are encoded in four operons (pmoCAB, mmoXYZBCD, mxaFI, and xoxF). Recent reports have suggested that methanotrophs in Proteobacteria acquired methane monooxygenases through horizontal gene transfer. Here, we used a genomic meta-analysis to infer the transcriptional and translational advantages of coding sequences from the methane oxidation metabolic modules of different types of methanotrophs. By analyzing isolate and metagenome-assembled genomes from phylogenetically and geographically diverse sources, we detected an anomalous nucleotide composition bias in the coding sequences of particulate methane monooxygenase genes (pmoCAB) from type Ia methanotrophs. We found that this nucleotide bias increases the level of codon bias by decreasing the GC content in the third base of codons, a strategy that contrasts with that of other coding sequences in the module. Further codon usage analyses uncovered that codon variants of the type Ia pmoCAB coding sequences deviate from the genomic signature to match ribosomal protein-coding sequences. Subsequently, computation of transcription and translation metrics revealed that the pmoCAB coding sequences of type Ia methanotrophs optimize the usage of codon variants to maximize translation efficiency and accuracy, while minimizing the synthesis cost of transcripts and proteins. IMPORTANCE Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.
format	article
author	Juan C. Villada Maria F. Duran Patrick K. H. Lee
author_facet	Juan C. Villada Maria F. Duran Patrick K. H. Lee
author_sort	Juan C. Villada
title	Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the <italic toggle="yes">pmoCAB</italic> Operon of Type Ia Methanotrophs
title_short	Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the <italic toggle="yes">pmoCAB</italic> Operon of Type Ia Methanotrophs
title_full	Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the <italic toggle="yes">pmoCAB</italic> Operon of Type Ia Methanotrophs
title_fullStr	Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the <italic toggle="yes">pmoCAB</italic> Operon of Type Ia Methanotrophs
title_full_unstemmed	Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the <italic toggle="yes">pmoCAB</italic> Operon of Type Ia Methanotrophs
title_sort	genomic evidence for simultaneous optimization of transcription and translation through codon variants in the <italic toggle="yes">pmocab</italic> operon of type ia methanotrophs
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/64c1460ee1ab4024ad814955c2ee9a31
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Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the <italic toggle="yes">pmoCAB</italic> Operon of Type Ia Methanotrophs

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