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1. Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria

   https://doi.org/10.1093/gbe/evac035  

   Grébert, Théophile ; Garczarek, Laurence ; Daubin, Vincent ; Humily, Florian ; Marie, Dominique ; Ratin, Morgane ; Devailly, Alban ; Farrant, Gregory K ; Mary, Isabelle ; Mella-Flores, Daniella ; et al ( April 2022 , Genome Biology and Evolution)

   Angert, Esther (Ed.)

   Synechococcus cyanobacteria are ubiquitous and abundant in the marine environment and contribute to an estimated 16% of the ocean net primary productivity. Their light-harvesting complexes, called phycobilisomes (PBS), are composed of a conserved allophycocyanin core, from which radiates six to eight rods with variable phycobiliprotein and chromophore content. This variability allows Synechococcus cells to optimally exploit the wide variety of spectral niches existing in marine ecosystems. Seven distinct pigment types or subtypes have been identified so far in this taxon based on the phycobiliprotein composition and/or the proportion of the different chromophores in PBS rods. Most genes involved in their biosynthesis and regulation are located in a dedicated genomic region called the PBS rod region. Here, we examine the variability of gene content and organization of this genomic region in a large set of sequenced isolates and natural populations of Synechococcus representative of all known pigment types. All regions start with a tRNA-PheGAA and some possess mobile elements for DNA integration and site-specific recombination, suggesting that their genomic variability relies in part on a “tycheposon”-like mechanism. Comparison of the phylogenies obtained for PBS and core genes revealed that the evolutionary history of PBS rod genes differs from the core genome and is characterized by the co-existence of different alleles and frequent allelic exchange. We propose a scenario for the evolution of the different pigment types and highlight the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in different Synechococcus lineages despite multiple speciation events.

    

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2. The phycoerythrobilin isomerization activity of MpeV in Synechococcus sp. WH8020 is prevented by the presence of a histidine at position 141 within its phycoerythrin-I β-subunit substrate

   https://doi.org/10.3389/fmicb.2022.1011189  

   Carrigee, Lyndsay A. ; Frick, Jacob P. ; Liu, Xindi ; Karty, Jonathan A. ; Trinidad, Jonathan C. ; Tom, Irin P. ; Yang, Xiaojing ; Dufour, Louison ; Partensky, Frédéric ; Schluchter, Wendy M. ( November 2022 , Frontiers in Microbiology)

   Marine Synechococcus efficiently harvest available light for photosynthesis using complex antenna systems, called phycobilisomes, composed of an allophycocyanin core surrounded by rods, which in the open ocean are always constituted of phycocyanin and two phycoerythrin (PE) types: PEI and PEII. These cyanobacteria display a wide pigment diversity primarily resulting from differences in the ratio of the two chromophores bound to PEs, the green-light absorbing phycoerythrobilin and the blue-light absorbing phycourobilin. Prior to phycobiliprotein assembly, bilin lyases post-translationally catalyze the ligation of phycoerythrobilin to conserved cysteine residues on α- or β-subunits, whereas the closely related lyase-isomerases isomerize phycoerythrobilin to phycourobilin during the attachment reaction. MpeV was recently shown in Synechococcus sp. RS9916 to be a lyase-isomerase which doubly links phycourobilin to two cysteine residues (C50 and C61; hereafter C50, 61) on the β-subunit of both PEI and PEII. Here we show that Synechococcus sp. WH8020, which belongs to the same pigment type as RS9916, contains MpeV that demonstrates lyase-isomerase activity on the PEII β-subunit but only lyase activity on the PEI β-subunit. We also demonstrate that occurrence of a histidine at position 141 of the PEI β-subunit from WH8020, instead of a leucine in its counterpart from RS9916, prevents the isomerization activity by WH8020 MpeV, showing for the first time that both the substrate and the enzyme play a role in the isomerization reaction. We propose a structural-based mechanism for the role of H141 in blocking isomerization. More generally, the knowledge of the amino acid present at position 141 of the β-subunits may be used to predict which phycobilin is bound at C50, 61 of both PEI and PEII from marine Synechococcus strains. 

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3. Molecular bases of an alternative dual-enzyme system for light color acclimation of marine Synechococcus cyanobacteria

   https://doi.org/10.1073/pnas.2019715118  

   Grébert, Théophile ; Nguyen, Adam A. ; Pokhrel, Suman ; Joseph, Kes Lynn ; Ratin, Morgane ; Dufour, Louison ; Chen, Bo ; Haney, Allissa M. ; Karty, Jonathan A. ; Trinidad, Jonathan C. ; et al ( February 2021 , Proceedings of the National Academy of Sciences)

   MarineSynechococcuscyanobacteria owe their ubiquity in part to the wide pigment diversity of their light-harvesting complexes. In open ocean waters, cells predominantly possess sophisticated antennae with rods composed of phycocyanin and two types of phycoerythrins (PEI and PEII). Some strains are specialized for harvesting either green or blue light, while others can dynamically modify their light absorption spectrum to match the dominant ambient color. This process, called type IV chromatic acclimation (CA4), has been linked to the presence of a small genomic island occurring in two configurations (CA4-A and CA4-B). While the CA4-A process has been partially characterized, the CA4-B process has remained an enigma. Here we characterize the function of two members of the phycobilin lyase E/F clan, MpeW and MpeQ, inSynechococcussp. strain A15-62 and demonstrate their critical role in CA4-B. While MpeW, encoded in the CA4-B island and up-regulated in green light, attaches the green light-absorbing chromophore phycoerythrobilin to cysteine-83 of the PEII α-subunit in green light, MpeQ binds phycoerythrobilin and isomerizes it into the blue light-absorbing phycourobilin at the same site in blue light, reversing the relationship of MpeZ and MpeY in the CA4-A strain RS9916. Our data thus reveal key molecular differences between the two types of chromatic acclimaters, both highly abundant but occupying distinct complementary ecological niches in the ocean. They also support an evolutionary scenario whereby CA4-B island acquisition allowed former blue light specialists to become chromatic acclimaters, while former green light specialists would have acquired this capacity by gaining a CA4-A island.

    

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4. A kinetic analysis of mouse rod and cone photoreceptor responses

   https://doi.org/10.1113/JP279524  

   Reingruber, Jürgen ; Ingram, Norianne T. ; Griffis, Khris G. ; Fain, Gordon L. ( July 2020 , The Journal of Physiology)

   Most vertebrate eyes have rods for dim‐light vision and cones for brighter light and higher temporal sensitivity.

   Rods evolved from cone‐like precursors through expression of different transduction genes or the same genes at different expression levels, but we do not know which molecular differences were most important.

   We approached this problem by analysing rod and cone responses with the same model but with different values for model parameters. We showed that, in addition to outer‐segment volume, the most important differences between rods and cones are: (1) decreased transduction gain, reflecting smaller amplification in the G‐protein cascade; (2) a faster rate of turnover of the second messenger cGMP in darkness; and (3) an accelerated rate of decay of the effector enzyme phosphodiesterase and perhaps also of activated visual pigment.

   We believe our analysis has identified the principal alterations during evolution responsible for the duplex retina.

   Most vertebrates have rod and cone photoreceptors, which differ in their sensitivity and response kinetics. We know that rods evolved from cone‐like precursors through the expression of different transduction genes or the same genes at different levels, but we do not know which molecular differences were most important. We have approached this problem in mouse retina by analysing the kinetic differences between rod flash responses and recent voltage‐clamp recordings of cone flash responses, using a model incorporating the principal features of photoreceptor transduction. We apply a novel method of analysis using the log‐transform of the current, and we ask which of the model's dynamic parameters need be changed to transform the flash response of a rod into that of a cone. The most important changes are a decrease in the gain of the response, reflecting a reduction in amplification of the transduction cascade; an increase in the rate of turnover of cGMP in darkness; and an increase in the rate of decay of activated phosphodiesterase, with perhaps also an increase in the rate of decay of light‐activated visual pigment. Although we cannot exclude other differences, and in particular alterations in the Ca²⁺economy of the photoreceptors, we believe that we have identified the kinetic parameters principally responsible for the differences in the flash responses of the two kinds of photoreceptors, which were likely during evolution to have resulted in the duplex retina.

    

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5. Photopigment, Absorption, and Growth Responses of Marine Cryptophytes to Varying Spectral Irradiance

   https://doi.org/10.1111/jpy.12962  

   Heidenreich, Kristin M. ; Richardson, Tammi L. ; Collier, ed., J. ( February 2020 , Journal of Phycology)

   The underwater light field of lakes, estuaries, and oceans may vary greatly in spectral composition. Phytoplankton in these environments must contain pigments that absorb the available colors of light. If spectral quality changes, acclimation to the new spectral environment would confer an ecological advantage in terms of photosynthesis and growth. Here, we explored the capacity of eight marine cryptophytes to adjust pigmentation in response to changes in spectral irradiance and related effects on light absorption, photosynthetically useable radiation (PUR), and growth rate. The pigment composition of all species changed in some way in response to shifts in spectral irradiance, but not all pigment changes could be considered advantageous in the context of chromatic acclimation. For most species, absorption by chl‐aand chl‐c₂resulted in highest absorption in the blue region, highestPURvalues for blue‐light grown cells, and highest growth rates in blue light. The exception wasChroomonas mesostigmatica(CCMP1168), which contains a high percentage of Cryptophyte‐Phycocyanin (Cr‐PC) 645, absorbs strongly in the orange‐to‐red region of the spectrum, and grew fastest under red light. The position and magnitude of the maximum and secondary absorption peak of Cr‐PC569, the phycobiliprotein pigment ofHemiselmis cryptochromatica, varied with spectral irradiance. The underlying cause remains unknown, but may represent a mechanism by which cryptophytes optimize photon capture.

    

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