Phylogenetic and Evolutionary Patterns in Microbial Carotenoid Biosynthesis Are Revealed by Comparative Genomics

BACKGROUND: Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data. METHODOLOGY/PRINCIPAL FINDINGS: Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family enzymes and carotenoid cyclases. Several phylogenetic lineage-specific evolutionary mechanisms are also suggested, including: (i) horizontal gene transfer; (ii) gene acquisition followed by differential gene loss; (iii) co-evolution with other biochemical structures such as proteorhodopsins; and (iv) positive selection. CONCLUSIONS/SIGNIFICANCE: Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident previously. This phylogenetic framework is applicable to understanding the evolution of specific carotenoid biosynthetic proteins or the unique characteristics of carotenoid biosynthetic evolution in a specific phylogenetic lineage. Together, these analyses suggest a "bramble" model for microbial carotenoid biosynthesis whereby later biosynthetic steps exhibit greater evolutionary plasticity and reticulation compared to those closer to the biosynthetic "root". Structural diversification may be constrained ("trimmed") where selection is strong, but less so where selection is weaker. These analyses also highlight likely productive avenues for future research and bioprospecting by identifying both gaps in current knowledge and taxa which may particularly facilitate carotenoid diversification

Spectroscopy of Photosynthetic Pigment-Protein Complex LHCII

Light-harvesting pigment-protein complex of photosystem II is the most abundant membrane protein in the biosphere, comprising more than half chlorophyll molecules. The protein plays a role of photosynthetic antenna, collecting solar radiation and transferring excitations towards the reaction centers, where electric charge separation takes place. Efficient excitation energy capture and transfer requires unique organization of the complex and unique photophysical properties of the accessory pigments: chlorophylls and carotenoids. LHCII is also a place where extremely harmful singlet oxygen may be generated, under strong illumination conditions. Several physical mechanisms have been found in LHCII, operating to protect the photosynthetic apparatus against light-induced damage, including chlorophyll triplet and singlet excitations quenching by carotenoids. In this paper we discuss the results of our recent studies, carried out with the application of several molecular spectroscopy techniques (electronic absorption, fluorescence, resonance Raman and FTIR), designed to investigate molecular mechanisms responsible for regulation of excitation density in LHCII. Among the most interesting findings are the light-induced molecular configuration changes of the LHCII-bound xanthophylls, leading to conformational rearrangements of the protein. These mechanisms are discussed in terms of excessive excitation quenching in the pigment-protein complex subjected to overexcitation. Such an activity seems to represent a vital regulatory process in the photosynthetic apparatus, at the molecular level, protecting plants against photodegradation

Spectroscopy of Photosynthetic Pigment-Protein Complex LHCII

Light-harvesting pigment-protein complex of photosystem II is the most abundant membrane protein in the biosphere, comprising more than half chlorophyll molecules. The protein plays a role of photosynthetic antenna, collecting solar radiation and transferring excitations towards the reaction centers, where electric charge separation takes place. Efficient excitation energy capture and transfer requires unique organization of the complex and unique photophysical properties of the accessory pigments: chlorophylls and carotenoids. LHCII is also a place where extremely harmful singlet oxygen may be generated, under strong illumination conditions. Several physical mechanisms have been found in LHCII, operating to protect the photosynthetic apparatus against light-induced damage, including chlorophyll triplet and singlet excitations quenching by carotenoids. In this paper we discuss the results of our recent studies, carried out with the application of several molecular spectroscopy techniques (electronic absorption, fluorescence, resonance Raman and FTIR), designed to investigate molecular mechanisms responsible for regulation of excitation density in LHCII. Among the most interesting findings are the light-induced molecular configuration changes of the LHCII-bound xanthophylls, leading to conformational rearrangements of the protein. These mechanisms are discussed in terms of excessive excitation quenching in the pigment-protein complex subjected to overexcitation. Such an activity seems to represent a vital regulatory process in the photosynthetic apparatus, at the molecular level, protecting plants against photodegradation

Nanoscale resolution in infrared imaging of protein-containing lipid membranes

The precise imaging of biomolecular entities contributes to an understanding of the relationship between their structure and function. However, the resolution of conventional infrared microscopic imaging is diffraction limited and does not exceed a few micrometres. Atomic force microscopy, on the other hand, can detect infrared absorption down to the sub-micrometer level. In the present report, we demonstrate that for multi-bilayer lipid samples containing the plant photosynthetic pigment-protein complex LHCII, the resolution of this latter technique can be better than 20 nm. Such a high resolution is attributable to two factors: (i) the relatively high infrared absorption by the complex that is integrated perpendicular to the plane of the multilayer film, and (ii) the distinctly different mechanical properties and thermal conductivity of the lipid and protein components of the sample

Analysis of the Site-Specific Myoglobin Modifications in the Melibiose-Derived Novel Advanced Glycation End-Product

MAGE (melibiose-derived advanced glycation end-product) is the glycation product generated in the reaction of a model protein with melibiose. The in vivo analog accumulates in several tissues; however, its origin still needs explanation. In vitro MAGE is efficiently generated under dry conditions in contrast to the reaction carried in an aqueous solvent. Using liquid chromatography coupled with mass spectrometry, we analyzed the physicochemical properties and structures of myoglobin glycated with melibiose under different conditions. The targeted peptide analysis identified structurally different AGEs, including crosslinking and non-crosslinking modifications associated with lysine, arginine, and histidine residues. Glycation in a dry state was more efficient in the formation of structures containing an intact melibiose moiety (21.9%) compared to glycation under aqueous conditions (15.6%). The difference was reflected in characteristic fluorescence that results from protein structural changes and impact on a heme group of the model myoglobin protein. Finally, our results suggest that the formation of in vitro MAGE adduct is initiated by coupling melibiose to a model myoglobin protein. It is confirmed by the identification of intact melibiose moieties. The intermediate glycation product can further rearrange towards more advanced structures, including cross-links. This process can contribute to a pool of AGEs accumulating locally in vivo and affecting tissue biology