Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature

Evolution; International Journal of Organic Evolution
Rohan MaddamsettiJustin R Meyer

Abstract

Viral gain-of-function mutations frequently evolve during laboratory experiments. Whether the specific mutations that evolve in the lab also evolve in nature and whether they have the same impact on evolution in the real world is unknown. We studied a model virus, bacteriophage λ, that repeatedly evolves to exploit a new host receptor under typical laboratory conditions. Here, we demonstrate that two residues of λ's J protein are required for the new function. In natural λ variants, these amino acid sites are highly diverse and evolve at high rates. Insertions and deletions at these locations are associated with phylogenetic patterns indicative of ecological diversification. Our results show that viral evolution in the laboratory mirrors that in nature and that laboratory experiments can be coupled with protein sequence analyses to identify the causes of viral evolution in the real world. Furthermore, our results provide evidence for widespread host-shift evolution in lambdoid viruses.

References

Jun 1, 2000·Proceedings of the National Academy of Sciences of the United States of America·K A Datsenko, B L Wanner
Dec 29, 2000·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·H A WichmanJ J Bull
Jul 27, 2002·Journal of Bacteriology·Forest Rohwer, Rob Edwards
Aug 17, 2002·Antimicrobial Agents and Chemotherapy·Barry G Hall
Dec 12, 2003·Nature·Rustom AntiaCarl T Bergstrom
Jan 7, 2004·Nature Reviews. Genetics·Andrew RambautEdward C Holmes
Apr 22, 2004·Nature Reviews. Microbiology·Barry G Hall
Jul 7, 2005·Journal of Molecular Evolution·Daniel E RozenRichard E Lenski
Jul 5, 2006·Molecular Biology and Evolution·Sergei L Kosakovsky PondSimon D W Frost
Mar 28, 2008·Molecular Biology and Evolution·Si Quang Le, Olivier Gascuel
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Apr 24, 2010·FEMS Microbiology Reviews·Merijn L M SalverdaMiriam Barlow
Nov 1, 2011·PLoS Computational Biology·Sean R Eddy
Dec 4, 2012·Viruses·Sujoy Chatterjee, Eli Rothenberg
Feb 23, 2013·PLoS Biology·Matthew D Herron, Michael Doebeli
Dec 3, 2013·Current Opinion in Genetics & Development·Daniel M WeinreichRobert B Heckendorn
Nov 7, 2014·PLoS Pathogens·Ben LongdonFrancis M Jiggins
Nov 16, 2014·Bioinformatics·Baris E SuzekUNKNOWN UniProt Consortium
Jan 21, 2015·Systematic Biology·Daniel L Rabosky, Emma E Goldberg
Mar 31, 2015·Journal of Molecular Biology·Natalia B Porcek, Kristin N Parent
May 7, 2015·Nucleic Acids Research·Robert D FinnSean R Eddy
Feb 20, 2016·Molecular Biology and Evolution·Kevin GoriChristophe Dessimoz
Feb 28, 2016·Molecular Biology and Evolution·Jaime Huerta-CepasPeer Bork
Jun 28, 2016·Nature Reviews. Microbiology·Emmie de WitVincent J Munster
Oct 14, 2016·Nature·Edward C HolmesKristian G Andersen
Nov 26, 2016·Science·Justin R MeyerRichard E Lenski
Jan 17, 2017·Nature Biotechnology·Thomas A HopfDebora S Marks
Mar 25, 2017·Cell·Adi SternRaul Andino
Apr 6, 2017·Genome Biology and Evolution·Rohan MaddamsettiRichard E Lenski
Apr 14, 2017·Cell Reports·Netanel TzarumIan A Wilson
Apr 22, 2017·Nucleic Acids Research·Szymon ChojnackiRodrigo Lopez

❮ Previous
Next ❯

Citations

Feb 17, 2021·The ISME Journal·Bryan Andrews, Stanley Fields

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR

Software Mentioned

Rate4Site
evcouplings
MAGE
HMMER
TreeCl
phmmer
LEISR
ETE Toolkit
FastTree

Related Concepts

Related Feeds

Bacteriophage: Phage Therapy

Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.

Researcher Network:CZI Neurodegeneration Challenge

The Neurodegeneration Challenge Network aims to provide funding for and to bring together researchers studying neurodegenerative diseases. Find the latest research from the NDCN grantees here.