8 Analytical Protocols in Phycobiliproteins Analysis
193
8.8 PBPs Identification by Proteomics
Using emerging proteomic methodologies, the most recent studies used global, and
especially differential proteomic analysis of cyanobacteria/algae, for investigation
of their circadian rhythm, cellular differentiation or acclimation to external/stress
factors and starvation focusing on the expression of PBPs. Proteomics was used
to investigate the link between light adaptation responses and phylogeny (different
strains) and pigmentation (different PBPs ratio) (Mackey et al. 2017), as well as to
monitor photo-acclimation by proteomics identification of expressed genes for PBPs
(Herrera-Salgado et al. 2018). PBPs degradation was followed by proteomics analysis during an organism’s adaptation to nitrogen depletion (Deschoenmaeker et al.
2014) and desiccation/rehydration (Xu et al. 2016). In an attempt to understand the
toxicity of herbicide butachlor, a proteomic approach was helpful for detection of
butachlor-induced down-regulation of PBPs (Kumari et al. 2009). Semiquantitative
proteomics was used to monitor the expression level of each of 20 PE subunits,
depending on light intensity during algal growth (Kieselbach et al. 2018). For quantitative proteomics, isobaric tags for relative and absolute quantitation (iTRAQ) were
exploited to reveal the capacity for transfer of light energy and expression of PBPs
during high-temperature stress and tolerance (Shi et al. 2017), as well as for monitoring of PBPs abundances in response to phosphate acclimation (Fuszard et al.
2013). In addition to label-free proteomics, quantitative proteomics with
14 N/
15 Nlabeled proteins was used for investigation of temperature-induced remodeling of the
photosynthetic machinery, where cells grown at high temperature were metabolically
labeled with
15 N (Nikolova et al. 2017). Phosphoproteomics, with the additional step
of phosphopeptides enrichment by TiO 2 chromatography, was exploited for detecting
how phosphorylation status of PBPs affects the energy transfer and state transition
of photosynthesis (Angeleri et al. 2016; Chen et al. 2015b). Spat et al. (2018) used
quantitative phosphoproteomics to describe the proteomic of a dormant cyanobacterium and its dynamics during the transition to vegetative growth, in order to find
the link between hyper-phosphorylation and the lifespan of PBPs during chlorosis.
On the other hand, high-resolution native mass spectrometry (NMS) which
preserves noncovalent interactions, enabled better insight into the adaptation of
the algal light-harvesting system to a wide range of environmental conditions via
oligomerization of PBPs (Eisenberg et al. 2017). The combination of NMS and
fluorescence spectroscopy was used to characterize the (dis)assembly of the PE
protein complex regarding species contributing to color and highly fluorescent properties of the complex (Leney et al. 2018). The major challenge in working with the
proteome of cyanobacteria is the high abundance of PBPs which affects the dynamic
detection range and therefore suppresses the MS identification of other proteins.
Matallana-Surget et al. (2014) successfully improved the cyanobacterial proteome
coverage using 3D LC-MS/MS approach. They introduced a immobilized Cu(II)affinity chromatography separation step to eliminate PBPs as the most abundant
193
8.8 PBPs Identification by Proteomics
Using emerging proteomic methodologies, the most recent studies used global, and
especially differential proteomic analysis of cyanobacteria/algae, for investigation
of their circadian rhythm, cellular differentiation or acclimation to external/stress
factors and starvation focusing on the expression of PBPs. Proteomics was used
to investigate the link between light adaptation responses and phylogeny (different
strains) and pigmentation (different PBPs ratio) (Mackey et al. 2017), as well as to
monitor photo-acclimation by proteomics identification of expressed genes for PBPs
(Herrera-Salgado et al. 2018). PBPs degradation was followed by proteomics analysis during an organism’s adaptation to nitrogen depletion (Deschoenmaeker et al.
2014) and desiccation/rehydration (Xu et al. 2016). In an attempt to understand the
toxicity of herbicide butachlor, a proteomic approach was helpful for detection of
butachlor-induced down-regulation of PBPs (Kumari et al. 2009). Semiquantitative
proteomics was used to monitor the expression level of each of 20 PE subunits,
depending on light intensity during algal growth (Kieselbach et al. 2018). For quantitative proteomics, isobaric tags for relative and absolute quantitation (iTRAQ) were
exploited to reveal the capacity for transfer of light energy and expression of PBPs
during high-temperature stress and tolerance (Shi et al. 2017), as well as for monitoring of PBPs abundances in response to phosphate acclimation (Fuszard et al.
2013). In addition to label-free proteomics, quantitative proteomics with
14 N/
15 Nlabeled proteins was used for investigation of temperature-induced remodeling of the
photosynthetic machinery, where cells grown at high temperature were metabolically
labeled with
15 N (Nikolova et al. 2017). Phosphoproteomics, with the additional step
of phosphopeptides enrichment by TiO 2 chromatography, was exploited for detecting
how phosphorylation status of PBPs affects the energy transfer and state transition
of photosynthesis (Angeleri et al. 2016; Chen et al. 2015b). Spat et al. (2018) used
quantitative phosphoproteomics to describe the proteomic of a dormant cyanobacterium and its dynamics during the transition to vegetative growth, in order to find
the link between hyper-phosphorylation and the lifespan of PBPs during chlorosis.
On the other hand, high-resolution native mass spectrometry (NMS) which
preserves noncovalent interactions, enabled better insight into the adaptation of
the algal light-harvesting system to a wide range of environmental conditions via
oligomerization of PBPs (Eisenberg et al. 2017). The combination of NMS and
fluorescence spectroscopy was used to characterize the (dis)assembly of the PE
protein complex regarding species contributing to color and highly fluorescent properties of the complex (Leney et al. 2018). The major challenge in working with the
proteome of cyanobacteria is the high abundance of PBPs which affects the dynamic
detection range and therefore suppresses the MS identification of other proteins.
Matallana-Surget et al. (2014) successfully improved the cyanobacterial proteome
coverage using 3D LC-MS/MS approach. They introduced a immobilized Cu(II)affinity chromatography separation step to eliminate PBPs as the most abundant