Exploring intrinsically disordered proteins in Chlamydomonas reinhardtii

Abstract

The content of intrinsically disordered protein (IDP) is related to organism complexity, evolution, and regulation. In the Plantae, despite their high complexity, experimental investigation of IDP content is lacking. We identified by mass spectrometry 682 heat-resistant proteins from the green alga, Chlamydomonas reinhardtii. Using a phosphoproteome database, we found that 331 of these proteins are targets of phosphorylation. We analyzed the flexibility propensity of the heat-resistant proteins and their specific features as well as those of predicted IDPs from the same organism. Their mean percentage of disorder was about 20%. Most of the IDPs (~70%) were addressed to other compartments than mitochondrion and chloroplast. Their amino acid composition was biased compared to other classic IDPs. Their molecular functions were diverse; the predominant ones were nucleic acid binding and unfolded protein binding and the less abundant one was catalytic activity. The most represented proteins were ribosomal proteins, proteins associated to flagella, chaperones and histones. We also found CP12, the only experimental IDP from C. reinhardtii that is referenced in disordered protein database. This is the first experimental investigation of IDPs in C. reinhardtii that also combines in silico analysis.

Evolutionary Study of Disorder in Protein Sequences

“…In Fungi and rest of Eukaryota, 14 and 6 species, respectively, stand out from the central cloud of data points with IDP fraction > 0.6 and IDR fraction > 0.2. Of these, six are Basidiomycota in Fungi, and, intriguingly, in the rest of Eukaryota we find 14 species all of which produce spores: 12 species of Apicomplexa, the choanoflagellate Salpingoeca rosetta (strain ATCC 50,818/BSB-021) and the single-cell green alga Chlamydomonas reinhardtii [ 31 ]). In Archaea there is a visibly distinct group containing species with high IDP and IDR fractions compared to the rest (IDP fraction > 0.2, IDR fraction > 0.05).…”

Desert cyanobacteria prepare in advance for dehydration and rewetting: The role of light and temperature sensing

“…The mechanisms whereby RNA (and possibly proteins) are stabilized/protected during desiccation (Figures and ) are as yet unknown. IDPs were implicated in the revival of Milnesium tardigradum following desiccation (Boothby et al, ) and in various algal activities (Gontero & Maberly, ; Niklas, Dunker, & Yruela, ; Zhang, Launay, Schramm, Lebrun, & Gontero, ). Many of the genes most strongly up‐regulated during early dehydration encode small, highly disordered, charged proteins.…”

Orchestration of algal metabolism by protein disorder

“…For instance, it has been shown that the activity of Calvin-Benson-Bassham (CBB) cycle enzymes is strongly affected by high pressure [61]. IDPs, which are devoid of internal cavities, are expected to be more stable upon pressure increase, and indeed, -synuclein [62] and the disordered region of titin [63] In the model alga Chlamydomonas reinhardtii, a systematic search for disordered protein experimentally showed that this alga contains a large number of non-characterised proteins that have IDP-like properties [72]. Interestingly, the few IDPs that have been biophysically investigated so far are the ones involved in the regulation of their metabolic pathways.…”

“…An experimental search for IDPs in C. reinhardtii showed that chaperones and ribosomal proteins were the most represented IDPs [72]. Twenty proteins related to chaperone-function were identified, such as the heat-shock proteins HSP33, HSP40, HSP70s, FKBP, HSP90 co-chaperone, ….…”

“…The experimental search for putative IDPs in C. reinhardtii also revealed few enzymes with long intrinsically disordered segments, involved in the algal metabolism ( Figure 6) that are nuclear-encoded and targeted to either the mitochondrion or the chloroplast [72]. These IDR-containing enzymes have not been studied so far to our knowledge.…”