The Use of a Chimeric Rhodopsin Vector for the Detection of New Proteorhodopsins Based on Color
Student microbial ecology laboratory courses are often conducted as condensed courses in which theory and wet lab work are combined in a very intensive short time period. In last decades, the study of marine microbial ecology is increasingly reliant on molecular-based methods, and as a result many o...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-03-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00439/full |
| _version_ | 1818110790992920576 |
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| author | Alina Pushkarev Gur Hevroni Sheila Roitman Jin-gon Shim Ahreum Choi Kwang-Hwan Jung Oded Béjà |
| author_facet | Alina Pushkarev Gur Hevroni Sheila Roitman Jin-gon Shim Ahreum Choi Kwang-Hwan Jung Oded Béjà |
| author_sort | Alina Pushkarev |
| collection | DOAJ |
| description | Student microbial ecology laboratory courses are often conducted as condensed courses in which theory and wet lab work are combined in a very intensive short time period. In last decades, the study of marine microbial ecology is increasingly reliant on molecular-based methods, and as a result many of the research projects conducted in such courses require sequencing that is often not available on site and may take more time than a typical course allows. In this work, we describe a protocol combining molecular and functional methods for analyzing proteorhodopsins (PRs), with visible results in only 4–5 days that do not rely on sequencing. PRs were discovered in oceanic surface waters two decades ago, and have since been observed in different marine environments and diverse taxa, including the abundant alphaproteobacterial SAR11 group. PR subgroups are currently known to absorb green and blue light, and their distribution was previously explained by prevailing light conditions – green pigments at the surface and blue pigments in deeper waters, as blue light travels deeper in the water column. To detect PR in environmental samples, we created a chimeric plasmid suitable for direct expression of PRs using PCR amplification and functional analysis in Escherichia coli cells. Using this assay, we discovered several exceptional cases of PRs whose phenotypes differed from those predicted based on sequence only, including a previously undescribed yellow-light absorbing PRs. We applied this assay in two 10-days marine microbiology courses and found it to greatly enhance students’ laboratory experience, enabling them to gain rapid visual feedback and colorful reward for their work. Furthermore we expect this assay to promote the use of functional assays for the discovery of new rhodopsin variants. |
| first_indexed | 2024-12-11T02:52:45Z |
| format | Article |
| id | doaj.art-a34a85ba1255488894fec4ecd8c33771 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-11T02:52:45Z |
| publishDate | 2018-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-a34a85ba1255488894fec4ecd8c337712022-12-22T01:23:15ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-03-01910.3389/fmicb.2018.00439331255The Use of a Chimeric Rhodopsin Vector for the Detection of New Proteorhodopsins Based on ColorAlina Pushkarev0Gur Hevroni1Sheila Roitman2Jin-gon Shim3Ahreum Choi4Kwang-Hwan Jung5Oded Béjà6Faculty of Biology, Technion – Israel Institute of Technology, Haifa, IsraelFaculty of Biology, Technion – Israel Institute of Technology, Haifa, IsraelFaculty of Biology, Technion – Israel Institute of Technology, Haifa, IsraelDepartment of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South KoreaDepartment of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South KoreaDepartment of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, South KoreaFaculty of Biology, Technion – Israel Institute of Technology, Haifa, IsraelStudent microbial ecology laboratory courses are often conducted as condensed courses in which theory and wet lab work are combined in a very intensive short time period. In last decades, the study of marine microbial ecology is increasingly reliant on molecular-based methods, and as a result many of the research projects conducted in such courses require sequencing that is often not available on site and may take more time than a typical course allows. In this work, we describe a protocol combining molecular and functional methods for analyzing proteorhodopsins (PRs), with visible results in only 4–5 days that do not rely on sequencing. PRs were discovered in oceanic surface waters two decades ago, and have since been observed in different marine environments and diverse taxa, including the abundant alphaproteobacterial SAR11 group. PR subgroups are currently known to absorb green and blue light, and their distribution was previously explained by prevailing light conditions – green pigments at the surface and blue pigments in deeper waters, as blue light travels deeper in the water column. To detect PR in environmental samples, we created a chimeric plasmid suitable for direct expression of PRs using PCR amplification and functional analysis in Escherichia coli cells. Using this assay, we discovered several exceptional cases of PRs whose phenotypes differed from those predicted based on sequence only, including a previously undescribed yellow-light absorbing PRs. We applied this assay in two 10-days marine microbiology courses and found it to greatly enhance students’ laboratory experience, enabling them to gain rapid visual feedback and colorful reward for their work. Furthermore we expect this assay to promote the use of functional assays for the discovery of new rhodopsin variants.http://journal.frontiersin.org/article/10.3389/fmicb.2018.00439/fullproteorhodopsinspectral tuningniche adaptationstudent laboratory coursesmarine microbiology |
| spellingShingle | Alina Pushkarev Gur Hevroni Sheila Roitman Jin-gon Shim Ahreum Choi Kwang-Hwan Jung Oded Béjà The Use of a Chimeric Rhodopsin Vector for the Detection of New Proteorhodopsins Based on Color Frontiers in Microbiology proteorhodopsin spectral tuning niche adaptation student laboratory courses marine microbiology |
| title | The Use of a Chimeric Rhodopsin Vector for the Detection of New Proteorhodopsins Based on Color |
| title_full | The Use of a Chimeric Rhodopsin Vector for the Detection of New Proteorhodopsins Based on Color |
| title_fullStr | The Use of a Chimeric Rhodopsin Vector for the Detection of New Proteorhodopsins Based on Color |
| title_full_unstemmed | The Use of a Chimeric Rhodopsin Vector for the Detection of New Proteorhodopsins Based on Color |
| title_short | The Use of a Chimeric Rhodopsin Vector for the Detection of New Proteorhodopsins Based on Color |
| title_sort | use of a chimeric rhodopsin vector for the detection of new proteorhodopsins based on color |
| topic | proteorhodopsin spectral tuning niche adaptation student laboratory courses marine microbiology |
| url | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00439/full |
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