Protein Homeostasis: How chloroplasts protect themselves from unfolded proteins

A genetic screen has identified the first signaling component of the unfolded protein response in chloroplasts.
  1. Felix Kessler  Is a corresponding author
  2. Paolo Longoni
  1. University of Neuchâtel, Switzerland

Eukaryotic cells contain organelles that perform specific roles. The chloroplasts in algae and plants, for example, harvest the energy from sunlight to produce organic molecules via photosynthesis. An organelle must import proteins from the cytoplasm to perform its role: however, these proteins have to be unfolded when they are imported, so they must be rapidly processed and folded once they are inside the organelle. If proteins that are not correctly folded accumulate, they can become toxic, and must be detected and removed in order to protect the organelle from damage.

A quality control system consisting of small heat shock proteins, chaperones and proteases ensures that all proteins entering the chloroplast are properly folded. However, when algae are exposed to high levels of light, or when a protease called ClpP1 is missing, this quality control system can become compromised and overwhelmed by unfolded proteins. This causes the chloroplast to trigger an ‘unfolded protein response’ (UPR) that upregulates the production of various proteins in the nucleus, which then travel to the chloroplast to help it cope with this overload of unfolded proteins. Although the UPR is well-understood in other organelles, such as the ER and mitochondria, the UPR in chloroplasts has been described to a far lesser degree. For example, it remains unclear how the chloroplast monitors the level of unfolded proteins and communicates this information to the nucleus.

Now, in eLife, Silvia Ramundo of the University of California San Francisco (UCSF) and colleagues – including Karina Perlaza as first author – report how they used a genetic screen to discover the first signaling component of chloroplast unfolded protein response (cpUPR) in the algae Chlamydomonas reinhardti (Perlaza et al., 2019). To create the screen, the researchers used an inducible switch that blocks the production of the ClpP1 protease: this blocking causes unfolded proteins to accumulate inside the chloroplast, triggering the cpUPR (Figure 1; Ramundo et al., 2014; Ramundo and Rochaix, 2014). To monitor the response, algae were engineered to express a fluorescent reporter that was under the control of a nuclear expressed gene that only becomes upregulated when the cpUPR is switched on. Perlaza et al. then inserted random mutations into the genome of these engineered algae, and screened for mutants that were no longer displaying fluorescence despite having activated the cpUPR (Figure 1).

The unfolded protein response in chloroplasts.

In wild-type C. reinhardti algae a protease called ClpP1 is responsible for removing unfolded proteins produced by stress (left). The loss of ClpP1 (right) leads to the accumulation of unfolded proteins in the chloroplast (dark green) triggering the cpUPR. This causes nuclear genes which encode factors that assist in protein folding (such as chaperones and proteases) to become upregulated. In order to monitor changes to cpUPR signaling, a fluorescent protein was put under the control of one of these factors (VIPP2), so that fluorescence could only be observed when cpUPR was induced. By inserting random mutations into the genome and screening for mutants no longer displaying the fluorescent reporter, Perlaza et al. were able to identify MARS1, a kinase involved in transmitting the cpUPR signal from the chloroplast to the nucleus. MARS1: mutant affected in chloroplast-to-nucleus retrograde signaling 1.

Using this screen, the team – which includes researchers from UCSF, the Lawrence Berkeley Lab and Princeton – identified a gene coding for a protein called MARS1 that is essential for activating the cpUPR. Because MARS1 was localized outside of the chloroplast and contained a kinase domain (a critical component of cell signaling), Perlaza et al. deduced that MARS1 is likely to be involved in sending the cpUPR signal from the chloroplast to the nucleus. Furthermore, mutating the catalytic residue within the kinase domain revealed that kinase activity was critical for the cpUPR.

Stress caused by high levels of sunlight leads to an increased production of reactive oxygen species (ROS) that damage proteins inside the chloroplast, which in turn triggers the cpUPR. Perlaza et al. found that mutating the kinase domain of MARS1 caused algae to be more susceptible to this type of chloroplast stress. Notably, the increased susceptibility of the mutants was only linked to chloroplast stressors that trigger the cpUPR, suggesting that MARS1 is specific for the unfolded protein response. Perlaza et al. also observed that mutant algae that had a dominantly active version of the kinase displayed enhanced resistance to high levels of light and ROS. This opens a potential avenue for how the cpUPR could be exploited to increase the efficiency of photosynthesis in other organisms.

The study of cpUPR is still in its infancy, but it is already revealing its importance in chloroplast development and the protection of photosynthetic activity. A crucial next step will be to apply this knowledge to higher plants, where MARS1 has not been identified but where responses equivalent to cpUPR have been shown to exist (Llamas et al., 2017). Any new components of the cpUPR pathway that researchers are able to identify could be potential new targets for increasing yields in crop species.


Article and author information

Author details

  1. Felix Kessler

    Felix Kessler is in the Laboratory of Plant Physiology, University of Neuchâtel, Neuchâtel, Switzerland

    For correspondence
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6409-5043
  2. Paolo Longoni

    Paolo Longoni is in the Laboratory of Plant Physiology, University of Neuchâtel, Neuchâtel, Switzerland

    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0587-7621

Publication history

  1. Version of Record published: October 15, 2019 (version 1)


© 2019, Kessler and Longoni



  • 1,675
    Page views
  • 175
  • 3


Download links


Downloads (link to download the article as PDF)



  1. Felix Kessler
  2. Paolo Longoni
Protein Homeostasis: How chloroplasts protect themselves from unfolded proteins
eLife 8:e51430.

Further reading

    1. Cell Biology
    Nozomu Yoshioka et al.
    Research Article

    Dystonin (DST), which encodes cytoskeletal linker proteins, expresses three tissue-selective isoforms: neural DST-a, muscular DST-b, and epithelial DST-e. DST mutations cause different disorders, including hereditary sensory and autonomic neuropathy 6 (HSAN-VI) and epidermolysis bullosa simplex; however, etiology of the muscle phenotype in DST-related diseases has been unclear. Because DST-b contains all of the DST-a-encoding exons, known HSAN-VI mutations could affect both DST-a and DST-b isoforms. To investigate the specific function of DST-b in striated muscles, we generated a Dst-b-specific mutant mouse model harboring a nonsense mutation. Dst-b mutant mice exhibited late-onset protein aggregate myopathy and cardiomyopathy without neuropathy. We observed desmin aggregation, focal myofibrillar dissolution, and mitochondrial accumulation in striated muscles, which are common characteristics of myofibrillar myopathy. We also found nuclear inclusions containing p62, ubiquitin, and SUMO proteins with nuclear envelope invaginations as a unique pathological hallmark in Dst-b mutation-induced cardiomyopathy. RNA-sequencing analysis revealed changes in expression of genes responsible for cardiovascular functions. In silico analysis identified DST-b alleles with nonsense mutations in populations worldwide, suggesting that some unidentified hereditary myopathy and cardiomyopathy are caused by DST-b mutations. Here, we demonstrate that the Dst-b isoform is essential for long-term maintenance of striated muscles.

    1. Cell Biology
    2. Neuroscience
    Lauritz Kennedy et al.
    Research Article

    Neonatal cerebral hypoxia-ischemia (HI) is the leading cause of death and disability in newborns with the only current treatment being hypothermia. An increased understanding of the pathways that facilitate tissue repair after HI may aid the development of better treatments. Here, we study the role of lactate receptor HCAR1 in tissue repair after neonatal HI in mice. We show that HCAR1 knockout mice have reduced tissue regeneration compared with wildtype mice. Furthermore, proliferation of neural progenitor cells and glial cells, as well as microglial activation was impaired. Transcriptome analysis showed a strong transcriptional response to HI in the subventricular zone of wildtype mice involving about 7300 genes. In contrast, the HCAR1 knockout mice showed a modest response, involving about 750 genes. Notably, fundamental processes in tissue repair such as cell cycle and innate immunity were dysregulated in HCAR1 knockout. Our data suggest that HCAR1 is a key transcriptional regulator of pathways that promote tissue regeneration after HI.