Analysing photosynthetic complexes in uncharacterized species or mixed microalgal communities using global antibodies

Photoautotrophs share core pathways for primary productivity and elemental cycling. These paths are generally mediated by abundant protein complexes which are conserved across wide taxonomic ranges, and which quantitatively dominate the proteomes of photoautotrophs. Quantification of key protein pools is a powerful approach to measure resource allocations and maximal catalytic capacities for biological functions, for comparing species or communities, or for tracking change over time within communities. Protein quantification can be more definitive than transcript analyses for functional studies, since changes in transcript levels are often only weakly coupled to pool sizes of functional protein. For field samples protein detections are more generally applicable than enzyme assays which require individually specialized extractions and assays, which are prone to interference by environmental contaminants. We are using bioinformatic analyses to design a series of peptide sequence tags that are conserved in all family members for a well-characterized subunit from each of the major catalytic complexes mediating photosynthesis and nitrogen metabolism. We use these peptide sequence tags to elicit production of 'global antibodies', intended to recognize all members of the target protein family with equal efficiency regardless of the species of origin. Uniform target detection is particularly important for tracking levels of key proteins in mixed communities, or for quantitative comparisons across plant species. In parallel we are creating quantification standards for these key protein pools for functional and (eco)physiological studies.