Functional and Systems Biology
Green Algae Routinely Transcribe Multiple Genes into One RNA Molecule
While transcription of multiple genes into one RNA molecule is common in bacteria, this process was thought to be rare in eukaryotes such as green algae.
Liquid cultures of Chlamydomonas reinhardtii are dark green from their abundant chlorophyll. RNA collected from this species revealed that many genes are grouped in functional clusters. Image by Anne Glaesener, U. C. Los Angeles | Stephanie King, PNNL
The Science
Every cell contains genes coded in its DNA. Genes are transcribed by cellular processes into a RNA molecule, which in turn is translated into a protein. Most bacteria, however, employ polycistronic transcription, meaning that several genes of related function are transcribed into a single RNA molecule. This multi-gene RNA is then translated into multiple proteins. Now, a study from a multi-institutional team of scientists reveals hundreds of examples where green algae use this method of transcription to produce multiple proteins simultaneously. The discovery of polycistronic gene expression in eukaryotic cells, such as algae, expands understanding of gene organization and transcription in organisms with a true nucleus.
The Impact
Some species of green algae have high quality, chromosome-scale genome assemblies. However, the annotation of individual features, such as genes, in these sequences is often incomplete. The discovery of widespread polycistronic transcripts in green algae has now led to the identification of hundreds of genes that standard gene-prediction algorithms had missed. This standard approach missed these genes because, for eukaryotic cells, these algorithms search genetic sequences assuming that each gene is transcribed into one RNA molecule.
Summary
A multi-institutional team of scientists studied the full-length transcripts from two species of green algae, Chlamydomonas reinhardtii and Chromochloris zofingiensis. They identified hundreds of examples of multiple genes transcribed on a single molecule of messenger RNA. Computational analyses marked individual protein-coding sections on the transcript and validated that this multi-gene transcription was not an artifact of the cellular RNA sequencing process. The scientists also measured whole cell proteomes to confirm that cells used the multi-gene transcripts to make proteins.
Examining five other green algae species revealed that this polycistronic gene expression is evolutionarily conserved over hundreds of millions of years, thus demonstrating its persistence and biological importance for survival. Eukaryotic polycistronic RNAs can also be a tool to design algal strains that produce biofuels and other bioproducts. A portion of this research was performed as a result of an award from the Facilities Integrating Collaborations for User Science (FICUS) program using resources at the Department of Energy (DOE) Joint Genome Institute (JGI) and EMSL, the Environmental Molecular Sciences Laboratory, which are DOE Office of Science user facilities. This work is part of EMSL’s Biomolecular Pathways Integrated Research Platform.
Contacts
Sabeeha S. Merchant, University of California, Berkeley, sabeeha@berkeley.edu
Sean D. Gallaher, University of California, Los Angeles, gallaher@chem.ucla.edu
Funding
This work was supported by the DOE Office of Science, Biological and Environmental Research program and the Basic Energy Sciences program. Proteomics analyses were performed under the FICUS program and used resources at the DOE JGI and EMSL.
Publications
S. D. Gallaher, et al., “Widespread polycistronic gene expression in green algae.” Proceedings of the National Academy of Sciences (2021). [DOI: 10.1073/pnas.2017714118]
Related Links
"Unexpected Algal Discoveries" DOE JGI video