Exploring Codon Adjustment Strategies towards Escherichia coli-Based Production of Viral Proteins Encoded by HTH1, a Novel Prophage of the Marine Bacterium Hypnocyclicus thermotrophus
Arsın, Hasan ; Jasilionis, Andrius LU ; Dahle, Håkon ; Sandaa, Ruth-Anne ; Stokke, Runar ; Nordberg Karlsson, Eva LU
and Steen, Ida Helene
(2021)
In Viruses
13(7).
- Abstract
Marine viral sequence space is immense and presents a promising resource for the discovery of new enzymes interesting for research and biotechnology. However, bottlenecks in the functional annotation of viral genes and soluble heterologous production of proteins hinder access to downstream characterization, subsequently impeding the discovery process. While commonly utilized for the heterologous expression of prokaryotic genes, codon adjustment approaches have not been fully explored for viral genes. Herein, the sequence-based identification of a putative prophage is reported from within the genome of Hypnocyclicus thermotrophus, a Gram-negative, moderately thermophilic bacterium isolated from the Seven Sisters hydrothermal vent... (More)
Marine viral sequence space is immense and presents a promising resource for the discovery of new enzymes interesting for research and biotechnology. However, bottlenecks in the functional annotation of viral genes and soluble heterologous production of proteins hinder access to downstream characterization, subsequently impeding the discovery process. While commonly utilized for the heterologous expression of prokaryotic genes, codon adjustment approaches have not been fully explored for viral genes. Herein, the sequence-based identification of a putative prophage is reported from within the genome of Hypnocyclicus thermotrophus, a Gram-negative, moderately thermophilic bacterium isolated from the Seven Sisters hydrothermal vent field. A prophage-associated gene cluster, consisting of 46 protein coding genes, was identified and given the proposed name Hypnocyclicus thermotrophus phage H1 (HTH1). HTH1 was taxonomically assigned to the viral family Siphoviridae, by lowest common ancestor analysis of its genome and phylogeny analyses based on proteins predicted as holin and DNA polymerase. The gene neighbourhood around the HTH1 lytic cassette was found most similar to viruses infecting Gram-positive bacteria. In the HTH1 lytic cassette, an N-acetylmuramoyl-L-alanine amidase (Amidase_2) with a peptidoglycan binding motif (LysM) was identified. A total of nine genes coding for enzymes putatively related to lysis, nucleic acid modification and of unknown function were subjected to heterologous expression in Escherichia coli. Codon optimization and codon harmonization approaches were applied in parallel to compare their effects on produced proteins. Comparison of protein yields and thermostability demonstrated that codon optimization yielded higher levels of soluble protein, but codon harmonization led to proteins with higher thermostability, implying a higher folding quality. Altogether, our study suggests that both codon optimization and codon harmonization are valuable approaches for successful heterologous expression of viral genes in E. coli, but codon harmonization may be preferable in obtaining recombinant viral proteins of higher folding quality.
(Less)
- author
- Arsın, Hasan
; Jasilionis, Andrius
LU
; Dahle, Håkon
; Sandaa, Ruth-Anne
; Stokke, Runar
; Nordberg Karlsson, Eva
LU
and Steen, Ida Helene
- organization
- publishing date
- 2021-06-23
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- prophage, hydrothermal vent, Hypnocyclicus thermotrophus, lytic cassette, Escherichia coli, heterologous expression, codon optimization, codon harmonization
- in
- Viruses
- volume
- 13
- issue
- 7
- article number
- 1215
- pages
- 21 pages
- publisher
- MDPI AG
- external identifiers
-
- pmid:34201869
- scopus:85109134836
- ISSN
- 1999-4915
- DOI
- 10.3390/v13071215
- language
- English
- LU publication?
- yes
- id
- f604c6c8-17d6-4787-beff-fd57b366073f
- date added to LUP
- 2021-07-14 00:11:07
- date last changed
- 2024-06-15 13:31:30
@article{f604c6c8-17d6-4787-beff-fd57b366073f,
abstract = {{<p>Marine viral sequence space is immense and presents a promising resource for the discovery of new enzymes interesting for research and biotechnology. However, bottlenecks in the functional annotation of viral genes and soluble heterologous production of proteins hinder access to downstream characterization, subsequently impeding the discovery process. While commonly utilized for the heterologous expression of prokaryotic genes, codon adjustment approaches have not been fully explored for viral genes. Herein, the sequence-based identification of a putative prophage is reported from within the genome of <i>Hypnocyclicus thermotrophus</i>, a Gram-negative, moderately thermophilic bacterium isolated from the Seven Sisters hydrothermal vent field. A prophage-associated gene cluster, consisting of 46 protein coding genes, was identified and given the proposed name <i>Hypnocyclicus thermotrophus</i> phage H1 (HTH1). HTH1 was taxonomically assigned to the viral family <i>Siphoviridae</i>, by lowest common ancestor analysis of its genome and phylogeny analyses based on proteins predicted as holin and DNA polymerase. The gene neighbourhood around the HTH1 lytic cassette was found most similar to viruses infecting Gram-positive bacteria. In the HTH1 lytic cassette, an N-acetylmuramoyl-L-alanine amidase (Amidase_2) with a peptidoglycan binding motif (LysM) was identified. A total of nine genes coding for enzymes putatively related to lysis, nucleic acid modification and of unknown function were subjected to heterologous expression in <i>Escherichia coli</i>. Codon optimization and codon harmonization approaches were applied in parallel to compare their effects on produced proteins. Comparison of protein yields and thermostability demonstrated that codon optimization yielded higher levels of soluble protein, but codon harmonization led to proteins with higher thermostability, implying a higher folding quality. Altogether, our study suggests that both codon optimization and codon harmonization are valuable approaches for successful heterologous expression of viral genes in <i>E. coli</i>, but codon harmonization may be preferable in obtaining recombinant viral proteins of higher folding quality.</p>}},
author = {{Arsın, Hasan and Jasilionis, Andrius and Dahle, Håkon and Sandaa, Ruth-Anne and Stokke, Runar and Nordberg Karlsson, Eva and Steen, Ida Helene}},
issn = {{1999-4915}},
keywords = {{prophage; hydrothermal vent; Hypnocyclicus thermotrophus; lytic cassette; Escherichia coli; heterologous expression; codon optimization; codon harmonization}},
language = {{eng}},
month = {{06}},
number = {{7}},
publisher = {{MDPI AG}},
series = {{Viruses}},
title = {{Exploring Codon Adjustment Strategies towards <i>Escherichia coli</i>-Based Production of Viral Proteins Encoded by HTH1, a Novel Prophage of the Marine Bacterium <i>Hypnocyclicus thermotrophus</i>}},
url = {{http://dx.doi.org/10.3390/v13071215}},
doi = {{10.3390/v13071215}},
volume = {{13}},
year = {{2021}},
}