<italic toggle="yes">De Novo</italic> Emergence of Peptides That Confer Antibiotic Resistance

ABSTRACT The origin of novel genes and beneficial functions is of fundamental interest in evolutionary biology. New genes can originate from different mechanisms, including horizontal gene transfer, duplication-divergence, and de novo from noncoding DNA sequences. Comparative genomics has generated...

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Autores principales:	Michael Knopp, Jonina S. Gudmundsdottir, Tobias Nilsson, Finja König, Omar Warsi, Fredrika Rajer, Pia Ädelroth, Dan I. Andersson
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	Escherichia coli antibiotic resistance aminoglycosides de novo gene evolution membrane potential Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/a465bd6ddd7943809361b427b9c043b8
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spelling	oai:doaj.org-article:a465bd6ddd7943809361b427b9c043b82021-11-15T15:55:25Z<italic toggle="yes">De Novo</italic> Emergence of Peptides That Confer Antibiotic Resistance10.1128/mBio.00837-192150-7511https://doaj.org/article/a465bd6ddd7943809361b427b9c043b82019-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00837-19https://doaj.org/toc/2150-7511ABSTRACT The origin of novel genes and beneficial functions is of fundamental interest in evolutionary biology. New genes can originate from different mechanisms, including horizontal gene transfer, duplication-divergence, and de novo from noncoding DNA sequences. Comparative genomics has generated strong evidence for de novo emergence of genes in various organisms, but experimental demonstration of this process has been limited to localized randomization in preexisting structural scaffolds. This bypasses the basic requirement of de novo gene emergence, i.e., lack of an ancestral gene. We constructed highly diverse plasmid libraries encoding randomly generated open reading frames and expressed them in Escherichia coli to identify short peptides that could confer a beneficial and selectable phenotype in vivo (in a living cell). Selections on antibiotic-containing agar plates resulted in the identification of three peptides that increased aminoglycoside resistance up to 48-fold. Combining genetic and functional analyses, we show that the peptides are highly hydrophobic, and by inserting into the membrane, they reduce membrane potential, decrease aminoglycoside uptake, and thereby confer high-level resistance. This study demonstrates that randomized DNA sequences can encode peptides that confer selective benefits and illustrates how expression of random sequences could spark the origination of new genes. In addition, our results also show that this question can be addressed experimentally by expression of highly diverse sequence libraries and subsequent selection for specific functions, such as resistance to toxic compounds, the ability to rescue auxotrophic/temperature-sensitive mutants, and growth on normally nonused carbon sources, allowing the exploration of many different phenotypes. IMPORTANCE De novo gene origination from nonfunctional DNA sequences was long assumed to be implausible. However, recent studies have shown that large fractions of genomic noncoding DNA are transcribed and translated, potentially generating new genes. Experimental validation of this process so far has been limited to comparative genomics, in vitro selections, or partial randomizations. Here, we describe selection of novel peptides in vivo using fully random synthetic expression libraries. The peptides confer aminoglycoside resistance by inserting into the bacterial membrane and thereby partly reducing membrane potential and decreasing drug uptake. Our results show that beneficial peptides can be selected from random sequence pools in vivo and support the idea that expression of noncoding sequences could spark the origination of new genes.Michael KnoppJonina S. GudmundsdottirTobias NilssonFinja KönigOmar WarsiFredrika RajerPia ÄdelrothDan I. AnderssonAmerican Society for MicrobiologyarticleEscherichia coliantibiotic resistanceaminoglycosidesde novogene evolutionmembrane potentialMicrobiologyQR1-502ENmBio, Vol 10, Iss 3 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Escherichia coli antibiotic resistance aminoglycosides de novo gene evolution membrane potential Microbiology QR1-502
spellingShingle	Escherichia coli antibiotic resistance aminoglycosides de novo gene evolution membrane potential Microbiology QR1-502 Michael Knopp Jonina S. Gudmundsdottir Tobias Nilsson Finja König Omar Warsi Fredrika Rajer Pia Ädelroth Dan I. Andersson <italic toggle="yes">De Novo</italic> Emergence of Peptides That Confer Antibiotic Resistance
description	ABSTRACT The origin of novel genes and beneficial functions is of fundamental interest in evolutionary biology. New genes can originate from different mechanisms, including horizontal gene transfer, duplication-divergence, and de novo from noncoding DNA sequences. Comparative genomics has generated strong evidence for de novo emergence of genes in various organisms, but experimental demonstration of this process has been limited to localized randomization in preexisting structural scaffolds. This bypasses the basic requirement of de novo gene emergence, i.e., lack of an ancestral gene. We constructed highly diverse plasmid libraries encoding randomly generated open reading frames and expressed them in Escherichia coli to identify short peptides that could confer a beneficial and selectable phenotype in vivo (in a living cell). Selections on antibiotic-containing agar plates resulted in the identification of three peptides that increased aminoglycoside resistance up to 48-fold. Combining genetic and functional analyses, we show that the peptides are highly hydrophobic, and by inserting into the membrane, they reduce membrane potential, decrease aminoglycoside uptake, and thereby confer high-level resistance. This study demonstrates that randomized DNA sequences can encode peptides that confer selective benefits and illustrates how expression of random sequences could spark the origination of new genes. In addition, our results also show that this question can be addressed experimentally by expression of highly diverse sequence libraries and subsequent selection for specific functions, such as resistance to toxic compounds, the ability to rescue auxotrophic/temperature-sensitive mutants, and growth on normally nonused carbon sources, allowing the exploration of many different phenotypes. IMPORTANCE De novo gene origination from nonfunctional DNA sequences was long assumed to be implausible. However, recent studies have shown that large fractions of genomic noncoding DNA are transcribed and translated, potentially generating new genes. Experimental validation of this process so far has been limited to comparative genomics, in vitro selections, or partial randomizations. Here, we describe selection of novel peptides in vivo using fully random synthetic expression libraries. The peptides confer aminoglycoside resistance by inserting into the bacterial membrane and thereby partly reducing membrane potential and decreasing drug uptake. Our results show that beneficial peptides can be selected from random sequence pools in vivo and support the idea that expression of noncoding sequences could spark the origination of new genes.
format	article
author	Michael Knopp Jonina S. Gudmundsdottir Tobias Nilsson Finja König Omar Warsi Fredrika Rajer Pia Ädelroth Dan I. Andersson
author_facet	Michael Knopp Jonina S. Gudmundsdottir Tobias Nilsson Finja König Omar Warsi Fredrika Rajer Pia Ädelroth Dan I. Andersson
author_sort	Michael Knopp
title	<italic toggle="yes">De Novo</italic> Emergence of Peptides That Confer Antibiotic Resistance
title_short	<italic toggle="yes">De Novo</italic> Emergence of Peptides That Confer Antibiotic Resistance
title_full	<italic toggle="yes">De Novo</italic> Emergence of Peptides That Confer Antibiotic Resistance
title_fullStr	<italic toggle="yes">De Novo</italic> Emergence of Peptides That Confer Antibiotic Resistance
title_full_unstemmed	<italic toggle="yes">De Novo</italic> Emergence of Peptides That Confer Antibiotic Resistance
title_sort	<italic toggle="yes">de novo</italic> emergence of peptides that confer antibiotic resistance
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/a465bd6ddd7943809361b427b9c043b8
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<italic toggle="yes">De Novo</italic> Emergence of Peptides That Confer Antibiotic Resistance

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