1
|
Gotsmann VL, Ting MKY, Haase N, Rudorf S, Zoschke R, Willmund F. Utilizing high-resolution ribosome profiling for the global investigation of gene expression in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1614-1634. [PMID: 38047591 DOI: 10.1111/tpj.16577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Ribosome profiling (Ribo-seq) is a powerful method for the deep analysis of translation mechanisms and regulatory circuits during gene expression. Extraction and sequencing of ribosome-protected fragments (RPFs) and parallel RNA-seq yields genome-wide insight into translational dynamics and post-transcriptional control of gene expression. Here, we provide details on the Ribo-seq method and the subsequent analysis with the unicellular model alga Chlamydomonas reinhardtii (Chlamydomonas) for generating high-resolution data covering more than 10 000 different transcripts. Detailed analysis of the ribosomal offsets on transcripts uncovers presumable transition states during translocation of elongating ribosomes within the 5' and 3' sections of transcripts and characteristics of eukaryotic translation termination, which are fundamentally distinct for chloroplast translation. In chloroplasts, a heterogeneous RPF size distribution along the coding sequence indicates specific regulatory phases during protein synthesis. For example, local accumulation of small RPFs correlates with local slowdown of psbA translation, possibly uncovering an uncharacterized regulatory step during PsbA/D1 synthesis. Further analyses of RPF distribution along specific cytosolic transcripts revealed characteristic patterns of translation elongation exemplified for the major light-harvesting complex proteins, LHCs. By providing high-quality datasets for all subcellular genomes and attaching our data to the Chlamydomonas reference genome, we aim to make ribosome profiles easily accessible for the broad research community. The data can be browsed without advanced bioinformatic background knowledge for translation output levels of specific genes and their splice variants and for monitoring genome annotation.
Collapse
Affiliation(s)
- Vincent Leon Gotsmann
- Molecular Genetics of Eukaryotes, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
| | - Michael Kien Yin Ting
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Nadin Haase
- Institute of Cell Biology and Biophysics, Leibniz University Hanover, Herrenhäuser-Str. 2, 30419, Hanover, Germany
| | - Sophia Rudorf
- Institute of Cell Biology and Biophysics, Leibniz University Hanover, Herrenhäuser-Str. 2, 30419, Hanover, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
| |
Collapse
|
2
|
Lee TM, Lin JY, Tsai TH, Yang RY, Ng IS. Clustered regularly interspaced short palindromic repeats (CRISPR) technology and genetic engineering strategies for microalgae towards carbon neutrality: A critical review. BIORESOURCE TECHNOLOGY 2023; 368:128350. [PMID: 36414139 DOI: 10.1016/j.biortech.2022.128350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Carbon dioxide is the major greenhouse gas and regards as the critical issue of global warming and climate changes. The inconspicuous microalgae are responsible for 40% of carbon fixation among all photosynthetic plants along with a higher photosynthetic efficiency and convert the carbon into lipids, protein, pigments, and bioactive compounds. Genetic approach and metabolic engineering are applied to accelerate the growth rate and biomass of microalgae, hence achieve the mission of carbon neutrality. Meanwhile, CRISPR/Cas9 is efficiently to enhance the productivity of high-value compounds in microalgae for it is easier operation, more affordable and is able to regulate multiple genes simultaneously. The genetic engineering strategies provide the multidisciplinary concept to evolute and increase the CO2 fixation rate through Calvin-Benson-Bassham cycle. Therefore, the technologies, bioinformatics tools, systematic engineering approaches for carbon neutrality and circular economy are summarized and leading one step closer to the decarbonization society in this review.
Collapse
Affiliation(s)
- Tse-Min Lee
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Jia-Yi Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Tsung-Han Tsai
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ru-Yin Yang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
| |
Collapse
|
3
|
Eckardt NA. From the archives: Photosynthesis matters; PSII antenna size, photorespiration, and the evolution of C4 photosynthesis. THE PLANT CELL 2022; 34:1145-1146. [PMID: 35234934 PMCID: PMC8972218 DOI: 10.1093/plcell/koac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Nancy A Eckardt
- Senior Features Editor, The Plant Cell, American Society of Plant Biologists, USA
| |
Collapse
|
4
|
Neofotis P, Temple J, Tessmer OL, Bibik J, Norris N, Pollner E, Lucker B, Weraduwage SM, Withrow A, Sears B, Mogos G, Frame M, Hall D, Weissman J, Kramer DM. The induction of pyrenoid synthesis by hyperoxia and its implications for the natural diversity of photosynthetic responses in Chlamydomonas. eLife 2021; 10:67565. [PMID: 34936552 PMCID: PMC8694700 DOI: 10.7554/elife.67565] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/13/2021] [Indexed: 12/31/2022] Open
Abstract
In algae, it is well established that the pyrenoid, a component of the carbon-concentrating mechanism (CCM), is essential for efficient photosynthesis at low CO2. However, the signal that triggers the formation of the pyrenoid has remained elusive. Here, we show that, in Chlamydomonas reinhardtii, the pyrenoid is strongly induced by hyperoxia, even at high CO2 or bicarbonate levels. These results suggest that the pyrenoid can be induced by a common product of photosynthesis specific to low CO2 or hyperoxia. Consistent with this view, the photorespiratory by-product, H2O2, induced the pyrenoid, suggesting that it acts as a signal. Finally, we show evidence for linkages between genetic variations in hyperoxia tolerance, H2O2 signaling, and pyrenoid morphologies.
Collapse
Affiliation(s)
- Peter Neofotis
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Joshua Temple
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States.,Department of Plant Biology, Michigan State University, East Lansing, United States
| | - Oliver L Tessmer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Jacob Bibik
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Nicole Norris
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Eric Pollner
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Ben Lucker
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Sarathi M Weraduwage
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States.,Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, United States
| | - Alecia Withrow
- Center for Advanced Microscopy, Michigan State University, East Lansing, United States
| | - Barbara Sears
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Greg Mogos
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Melinda Frame
- Center for Advanced Microscopy, Michigan State University, East Lansing, United States
| | - David Hall
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Joseph Weissman
- Corporate Strategic Research, ExxonMobil, Annandale, United States
| | - David M Kramer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| |
Collapse
|