Publications

In Press
Guo-Wei Qiu, Coco Koedooder, Bao-Sheng Qiu, Yeala Shaked, and Nir Keren. In Press. “Iron transport in cyanobacteria – from molecules to communities.” Trends in Microbiology. Abstract
Iron is an essential micronutrient for the ecologically important photoautotrophic cyanobacteria which are found across diverse aquatic environments. Low concentrations and poor bioavailability of certain iron species exert a strong control on cyanobacterial growth, affecting ecosystem structure and biogeochemical cycling. Here, we review the iron-acquisition pathways cyanobacteria utilize for overcoming these challenges. As the molecular details of cyanobacterial iron transport are being uncovered, an overall scheme of how cyanobacteria handle and exploit this scarce and redox-active micronutrient is emerging. Importantly, the range of biological solutions used by cyanobacteria to increase iron fluxes goes beyond transport and includes behavioral traits of colonial cyanobacteria and intricate cyanobacteria?bacteria interactions.Iron is an essential micronutrient for the ecologically important photoautotrophic cyanobacteria which are found across diverse aquatic environments. Low concentrations and poor bioavailability of certain iron species exert a strong control on cyanobacterial growth, affecting ecosystem structure and biogeochemical cycling. Here, we review the iron-acquisition pathways cyanobacteria utilize for overcoming these challenges. As the molecular details of cyanobacterial iron transport are being uncovered, an overall scheme of how cyanobacteria handle and exploit this scarce and redox-active micronutrient is emerging. Importantly, the range of biological solutions used by cyanobacteria to increase iron fluxes goes beyond transport and includes behavioral traits of colonial cyanobacteria and intricate cyanobacteria?bacteria interactions.
2021
Guo-Wei Qiu, Hagar Lis, Bao-Sheng Qiu, and Nir Keren. 2021. “Long-term iron deprivation and subsequent recovery uncover heterogeneity in the response of cyanobacterial populations.” Environmental Microbiology, 23, 3, Pp. 1793-1804. Abstract
Summary Cyanobacteria are globally important primary producers and nitrogen fixers. They are frequently limited by iron bioavailability in natural environments that often fluctuate due to rapid consumption and irregular influx of external Fe. Here we identify a succession of physiological changes in Synechocystis sp. PCC 6803 occurring over 14–16 days of iron deprivation and subsequent recovery. We observe several adaptive strategies that allow cells to push their metabolic limits under the restriction of declining intracellular Fe quotas. Interestingly, cyanobacterial populations exposed to prolonged iron deprivation showed discernible heterogeneity in cellular auto-fluorescence during the recovery process. Using FACS and microscopy techniques we revealed that only cells with high auto-fluorescence were able to grow and reconstitute thylakoid membranes. We propose that ROS-mediated damage is likely to be associated with the emergence of the two subpopulations, and, indeed, a rapid increase in intracellular ROS content was observed during the first hours following iron addition to Fe-starved cultures. These results suggest that an increasing iron supply is a double-edged sword - posing both an opportunity and a risk. Therefore, phenotypic heterogeneity within populations is crucial for the survival and proliferation of organisms facing iron fluctuations within natural environments.
Yuval Kolodny, Hagit Zer, Mor Propper, Shira Yochelis, Yossi Paltiel, and Nir Keren. 2021. “Marine cyanobacteria tune energy transfer efficiency in their light-harvesting antennae by modifying pigment coupling.” The FEBS Journal, 288, 3, Pp. 980-994. Abstract
Photosynthetic light harvesting is the first step in harnessing sunlight toward biological productivity. To operate efficiently under a broad and dynamic range of environmental conditions, organisms must tune the harvesting process according to the available irradiance. The marine cyanobacteria Synechococcus WH8102 species is well-adapted to vertical mixing of the water column. By studying its responses to different light regimes, we identify a new photo-acclimation strategy. Under low light, the phycobilisome (PBS) is bigger, with extended rods, increasing the absorption cross-section. In contrast to what was reported in vascular plants and predicted by Forster resonance energy transfer (FRET) calculations, these longer rods transfer energy faster than in the phycobilisomes of cells acclimated to a higher light intensity. Comparison of cultures grown under different blue light intensities, using fluorescence lifetime and emission spectra dependence on temperature at the range of 4–200 K in vivo, indicates that the improved transfer arises from enhanced energetic coupling between the antenna rods' pigments. We suggest two physical models according to which the enhanced coupling strength results either from additional coupled pathways formed by rearranging rod packing or from the coupling becoming non-classical. In both cases, the energy transfer would be more efficient than standard one-dimensional FRET process. These findings suggest that coupling control can be a major factor in photosynthetic antenna acclimation to different light conditions.
Tomáš Zavřel, Hanan Schoffman, Martin Lukeš, Jan Fedorko, Nir Keren, and Jan Červený. 2021. “Monitoring fitness and productivity in cyanobacteria batch cultures.” Algal Research, 56, Pp. 102328. Abstract
Cyanobacteria are key photosynthetic organisms in many aquatic ecosystems and hold great potential for sustainable green biotechnology. Growth of cyanobacteria in batch cultures is expected to be part of future biotechnological practices. However, the issue of correlating the dynamics of metabolic and photosynthetic parameters with the culture fitness during batch cultivation is still outstanding. In this paper we take advantage of a photobioreactor system to continuously track growth parameters of Synechocystis sp. PCC 6803, and to couple online culture monitoring with offline measurements of photosynthetic efficiency and biochemical and elemental cell composition under several light intensity and CO2 regimes. Light intensity determines the flux of energy into the photosynthetic system while CO2 concentrations determines the ability to capture this energy in chemical form. From this perspective, four distinct source-sink regimes were established and compared, which allowed us to reveal specific strategies to acclimate to both carbon and light limitation. As part of the measurements, room temperature excitation-emission spectra and elemental composition of Synechocystis cells were, for the first time, compared throughout the exponential and linear growth phases. In total, 39 parameters (out of 170 measured) were identified as highly correlating (R2 > 0.9) with growth rate or productivity under at least one tested cultivation condition, including concentrations and ratios of pigments or particular elements. For online fitness and productivity monitoring in cyanobacteria batch cultures, parameters such as photosynthesis and respiration rates and ratios, energy-dependent non-photochemical quenching (qE) or Zn and Mo concentration in the cultivation medium can be of interest.
2020
Guo‐Wei Qiu, Hai‐Bo Jiang, Hagar Lis, Zheng‐Ke Li, Bin Deng, Jin‐Long Shang, Chuan‐Yu Sun, Nir Keren, and Bao‐Sheng Qiu. 11/2020. “A unique porin meditates iron selective transport through cyanobacterial outer membranes.” Environmental Microbiology. Publisher's Version Abstract
Cyanobacteria are globally important primary producers and nitrogen fixers with high iron demands. Low ambient dissolved iron concentrations in many aquatic environments mean that these organisms must maintain sufficient and selective transport of iron into the cell. However, the nature of iron transport pathways through the cyanobacterial outer membrane remains obscure. Here we present multiple lines of experimental evidence that collectively support the existence of a novel class of substrate‐selective iron porin, Slr1908, in the outer membrane of the cyanobacterium Synechocystis sp. PCC 6803. Elemental composition analysis and short‐term iron uptake assays with mutants in Slr1908 reveal that this protein is primarily involved in inorganic iron uptake and contributes less to the accumulation of other metals. Homologs of Slr1908 are widely distributed in both freshwater and marine cyanobacteria, most notably in unicellular marine diazotrophs. Complementary experiments with a homolog of Slr1908 in Synechococcus PCC 7002 restored the phenotype of Synechocystis knockdown mutants, showing that this siderophore producing species also possesses a porin with a similar function in Fe transport. The involvement of a substrate‐selective porins in iron uptake may allow cyanobacteria to tightly control iron flux into the cell, particularly in environments where iron concentrations fluctuate.
Hanan Schoffman, William M. Brown, Yossi Paltiel, Nir Keren, and Erik M. Gauger. 8/26/2020. “Structure-based Hamiltonian model for IsiA uncovers a highly robust pigment protein complex.” Journal of The Royal Society Interface, 17, Pp. 20200399. Abstract
The iron stress-induced protein A (IsiA) is a source of interest and debate in biological research. The IsiA super-complex, binding over 200 chlorophylls, assembles in multimeric rings around photosystem I (PSI). Recently, the IsiA-PSI structure was resolved to 3.48 Å. Based on this structure, we created a model simulating a single excitation event in an IsiA monomer. This model enabled us to calculate the fluorescence and the localisation of the excitation in the IsiA structure. To further examine this system, noise was introduced to the model in two forms -- thermal and positional. Introducing noise highlights the functional differences in the system between cryogenic temperatures and biologically relevant temperatures. Our results show that the energetics of the IsiA pigment-protein complex are very robust at room temperature. Nevertheless, shifts in the position of speci
Stephane Martinez, Yuval Kolodny, Eli Shemesh, Federica Scucchia, Reinat Nevo, Smadar Levin-Zaidman, Yossi Paltiel, Nir Keren, Dan Tchernov, and Tali Mass. 2020. “Energy sources of the depth-generalist mixotrophic coral Stylophora pistillata.” Frontiers in Marine Science, 7, Pp. 988. Abstract
Energy sources of corals, ultimately sunlight and plankton availability, change dramatically from shallow to mesophotic (30–150 m) reefs. Depth-generalist corals, those that occupy both of these two distinct ecosystems, are adapted to cope with such extremely diverse conditions. In this study, we investigated the trophic strategy of the depth-generalist hermatypic coral Stylophora pistillata and the ability of mesophotic colonies to adapt to shallow reefs. We compared symbiont genera composition, photosynthetic traits and the holobiont trophic position and carbon sources, calculated from amino acids compound-specific stable isotope analysis (AA-CSIA), of shallow, mesophotic and translocated corals. This species harbors different Symbiodiniaceae genera at the two depths: Cladocopium goreaui (dominant in mesophotic colonies) and Symbiodinium microadriaticum (dominant in shallow colonies) with a limited change after transplantation. This allowed us to determine which traits stem from hosting different symbiont species compositions across the depth gradient. Calculation of holobiont trophic position based on amino acid δ15N revealed that heterotrophy represents the same portion of the total energy budget in both depths, in contrast to the dogma that predation is higher in corals growing in low light conditions. Photosynthesis is the major carbon source to corals growing at both depths, but the photosynthetic rate is higher in the shallow reef corals, implicating both higher energy consumption and higher predation rate in the shallow habitat. In the corals transplanted from deep to shallow reef, we observed extensive photo-acclimation by the Symbiodiniaceae cells, including substantial cellular morphological modifications, increased cellular chlorophyll a, lower antennae to photosystems ratios and carbon signature similar to the local shallow colonies. In contrast, non-photochemical quenching remains low and does not increase to cope with the high light regime of the shallow reef. Furthermore, host acclimation is much slower in these deep-to-shallow transplanted corals as evident from the lower trophic position and tissue density compared to the shallow-water corals, even after long-term transplantation (18 months). Our results suggest that while mesophotic reefs could serve as a potential refuge for shallow corals, the transition is complex, as even after a year and a half the acclimation is only partial.
Ketty Margulis, Hagit Zer, Hagar Lis, Hanan Schoffman, Omer Murik, Ginga Shimakawa, Anja Krieger-Liszkay, and Nir Keren. 2020. “Over Expression of the Cyanobacterial Pgr5-Homologue Leads to Pseudoreversion in a Gene Coding for a Putative Esterase in Synechocystis 6803.” Life, 10, Pp. 10.3390/life10090174 . Abstract
Pgr5 proteins play a major direct role in cyclic electron flow paths in plants and eukaryotic phytoplankton. The genomes of many cyanobacterial species code for Pgr5-like proteins but their function is still uncertain. Here, we present evidence that supports a link between the Synechocystis sp. PCC6803 Pgr5-like protein and the regulation of intracellular redox balance. The knockout strain, pgr5KO, did not display substantial phenotypic response under our experimental conditions, confirming results obtained in earlier studies. However, the overexpression strain, pgr5OE, accumulated 2.5-fold more chlorophyll than the wild type and displayed increased content of photosystems matching the chlorophyll increase. As a result, electron transfer rates through the photosynthetic apparatus of pgr5OE increased, as did the amount of energy stored as glycogen. While, under photoautotrophic conditions, this metabolic difference had only minor effects, under mixotrophic conditions, pgr5OE cultures collapsed. Interestingly, this specific phenotype of pgr5OE mutants displayed a tendency for reverting, and cultures which previously collapsed in the presence of glucose were now able to survive. DNA sequencing of a pgr5OE strain revealed a second site suppression mutation in slr1916, a putative esterase associated with redox regulation. The phenotype of the slr1916 knockout is very similar to that of the strain reported here and to that of the pmgA regulator knockout. These data demonstrate that, in Synechocystis 6803, there is strong selection against overexpression of the Pgr5-like protein. The pseudoreversion event in a gene involved in redox regulation suggests a connection of the Pgr5-like protein to this network.
Or Ben-Zvi, Raz Tamir, Nir Keren, Dan Tchernov, Ilana Berman-Frank, Yuval Kolodny, Tal Benaltabet, Harel Bavli, Mor Friedman, Noga Glanz-Idan, Hadar Traugott, Yossi Loya, and Gal Eyal. 2020. “Photophysiology of a mesophotic coral 3 years after transplantation to a shallow environment.” Coral Reefs, Pp. 1-11. Abstract
With shallow coral reefs suffering from anongoing rapid decline in many regions of the world, theinterest in studies on mesophotic coral ecosystems(30–150 m) is growing rapidly. While most photoaccli-mation responses in corals were documented within theupper 30 m of reefs, in the present study we transplantedfragments of a strictly mesophotic species from the RedSea,Euphyllia paradivisa, from 50 m to 5 m for a periodof 3 years. Following the retrieval of the corals, theirphysiological and photosynthetic properties of the coralswere tested. The transplanted corals presented evidence ofphotosynthetic acclimation to the shallow habitat, lowersensitivity to photoinhibition, and a high survival per-centage, while also demonstrating a reduced ability toutilize low light compared to their mesophotic counter-parts. This long-term successful transplantation from amesophotic depth to a shallow habitat has provided us withinsights regarding the ability of mesophotic corals and theirsymbionts to survive and withstand shallow environments,dominated by a completely different light regime. Theextensive characterization of the photobiology ofE.paradivisa, and its photoacclimation response to a high-light environment also demonstrates the plasticity of coralsand point out to mechanisms different than those reportedpreviously in shallower corals.
Reza Ranjbar Choubeh, Leeat Bar-Eyal, Yossi Paltiel, Nir Keren, Paul C Struik, and Herbert van Amerongen. 2020. “Photosystem II core quenching in desiccated Leptolyngbya ohadii.” Photosynthesis research, 143, Pp. 13-18. Abstract
Cyanobacteria living in the harsh environment of the desert have to protect themselves against high light intensity and prevent photodamage. These cyanobacteria are in a desiccated state during the largest part of the day when both temperature and light intensity are high. In the desiccated state, their photosynthetic activity is stopped, whereas upon rehydration the ability to perform photosynthesis is regained. Earlier reports indicate that light-induced excitations in Leptolyngbya ohadii are heavily quenched in the desiccated state, because of a loss of structural order of the light-harvesting phycobilisome structures (Bar Eyal et al. in Proc Natl Acad Sci 114:9481, 2017) and via the stably oxidized primary electron donor in photosystem I, namely P700+ (Bar Eyal et al. in Biochim Biophys Acta Bioenergy 1847:1267–1273, 2015). In this study, we use picosecond fluorescence experiments to demonstrate that a third protection mechanism exists, in which the core of photosystem II is quenched independently.
2019
Hanan Schoffman and Nir Keren. 2019. “Function of the IsiA pigment–protein complex in vivo.” Photosynthesis research, 141, 3, Pp. 343-353.
2018
Sofia Shevtsov, Omer Murik, Hagit Zer, Ofir Weinstein, Nir Keren, Ori Fragman-Sapir, and Oren Ostersetzer-Biran. 2018. “The complete plastid genome sequence and the photosynthetic activity of the putative mycoheterotrophic orchid Limodorum abortivum.” Israel Journal of Plant Sciences, 1, aop, Pp. 1–20.
Noam Adir, Nir Keren, Yossi Paltiel, ANAT SHPERBERG-AVNI, and Leeat Bar-Eyal. 2018. “Light harvesting in cyanobacteria: The phycobilisomes.” In Light Harvesting in Photosynthesis, Pp. 91–108. CRC Press.
Hagar Lis, Tal Weiner, Frances D Pitt, Nir Keren, and Alon Angert. 2018. “Phosphate Uptake by Cyanobacteria Is Associated with Kinetic Fractionation of Phosphate Oxygen Isotopes.” ACS Earth and Space Chemistry, 3, 2, Pp. 233–239.
Nir Keren and Yossi Paltiel. 2018. “Photosynthetic energy transfer at the quantum/classical border.” Trends in plant science, 23, 6, Pp. 497–506.
Hagit Zer, Ketty Margulis, Jens Georg, Yoram Shotland, Gergana Kostova, Laure D Sultan, Wolfgang R Hess, and Nir Keren. 2018. “Resequencing of a mutant bearing an iron starvation recovery phenotype defines Slr1658 as a new player in the regulatory network of a model cyanobacterium.” The Plant Journal, 93, 2, Pp. 235–245.
2017
Leeat Bar Eyal, Reza Ranjbar Choubeh, Eyal Cohen, Ido Eisenberg, Carmen Tamburu, Márta Dorogi, Renata Ünnep, Marie-Sousai Appavou, Reinat Nevo, Uri Raviv, and others. 2017. “Changes in aggregation states of light-harvesting complexes as a mechanism for modulating energy transfer in desert crust cyanobacteria.” Proceedings of the National Academy of Sciences, 114, 35, Pp. 9481–9486.
Ido Eisenberg, Dvir Harris, Yael Levi-Kalisman, Shira Yochelis, Asaf Shemesh, Gili Ben-Nissan, Michal Sharon, Uri Raviv, Noam Adir, Nir Keren, and others. 2017. “Concentration-based self-assembly of phycocyanin.” Photosynthesis research, 134, 1, Pp. 39–49.
Yael Kurzweil-Segev, Ivan Popov, Ido Eisenberg, Shira Yochelis, Nir Keren, Yossi Paltiel, and Yuri Feldman. 2017. “Confined water dynamics in a hydrated photosynthetic pigment–protein complex.” Physical Chemistry Chemical Physics, 19, 41, Pp. 28063–28070.
Nadav Oren, Hagai Raanan, Omer Murik, Nir Keren, and Aaron Kaplan. 2017. “Dawn illumination prepares desert cyanobacteria for dehydration.” Current Biology, 27, 19, Pp. R1056–R1057.

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