Biology subjects

Allahverdiyeva, Y.

Publications and source records attributed to Allahverdiyeva, Y..

12 recordsLinked to original sources

bioRxiv2026

A conserved photosynthetic cytochrome enhances growth in fluctuating light

Having at least one of the small soluble electron carriers cytochrome c6 (c6) and plastocyanin is indispensable for photosynthesis. It was believed that c6 had been lost from plants until a ubiquitous and highly conserved homologue, now named cytochrome c6A (c6A), was found in Arabidopsis thaliana. In spite of an early suggestion that c6A functioned like c6 in the photosynthetic electron transport chain it was soon shown to be unable to do so despite the strong structural homology between the two proteins. The function of c6A, and why it is apparently universal in plants and green algae, therefore remained unknown. Here, we show that, in the green alga Chlamydomonas reinhardtii, c6A confers a growth advantage under fluctuating light and is crucial for maintaining the light harvesting balance between photosystems I and II in photomixotrophic conditions. We show that in the absence of c6A, the light harvesting balance shifts towards PSII, leading to a more reduced plastoquinone pool and increased photooxidative stress. This study provides insights into how photosynthetic organisms acclimatize to stressful light conditions, indicating that c6A is important for this adaptation. These findings provide a basis for further mechanistic studies on a hypothesized role for c6A in thiol-based redox regulation in the thylakoid lumen, with implications for photoprotection mechanisms such as state transitions.

plant biology↗

bioRxiv2025

Over four months of ethylene production: Unlocking the potential of solid-state photosynthetic cell factories

This study demonstrates the feasibility of employing solid-state photosynthetic cell factories (solid-state PCFs) as a proof-of-concept platform for long-term ethylene production using sodium bicarbonate as the carbon source. Solid-state PCFs were constructed by entrapping Synechocystis sp. PCC 6803 (efe mutant, strain S5), specifically engineered for ethylene biosynthesis, within TEMPO-oxidized cellulose nanofiber (TCNF) matrices. Two distinct formulations were tested: (i) Ca2+-PVA-TCNF, in which TCNF was crosslinked with Ca2+ and polyvinyl alcohol to produce hydrogel films approximately 200 m thick; and (ii) an all-polysaccharide-based Ca2+-MLG-TCNF formulation, in which TCNF was crosslinked with Ca2+ and mixed-linkage glucan. The latter films were fabricated using an osmotic dehydration approach, yielding mechanically robust, fully biodegradable structures with a thickness of approximately 2 mm. The integration of engineered cells with TCNF matrices created a biocatalytic system that improved the distribution of light, nutrients, and substrates to the cells, while facilitating ethylene separation, thereby supporting the fitness of immobilized cells and enhancing their metabolic performance. Using a custom-designed photobiofilm reactor optimized for semi-wet cultivation, the solid-state PCFs sustained ethylene production for over four months, representing the longest reported continuous ethylene production by cyanobacteria to date. Notably, the solid-state PCFs achieved up to a twofold increase in ethylene yield compared to the continuous-flow suspension culture. Importantly, the suspension-based system also represented the first demonstration of four-month ethylene production under continuous-flow operation. In addition, biodegradability assessments confirmed the environmental compatibility of the TCNF-based matrices, with the all-polysaccharide formulation being particularly advantageous due to its exclusively nature-based composition. Together, these results demonstrate the potential of solid-state PCFs as a scalable and sustainable platform for photosynthetic ethylene production.

bioengineering↗

bioRxiv2025

Plastoquinone redox status influences carboxysome integrity via a RpaA- and ROS-dependent regulatory network

Carboxysomes are bacterial microcompartments that encapsulate Rubisco and are a core component of the cyanobacterial carbon concentration mechanism (CCM). While carboxysome number, size and spatial organization are observed to vary in different environmental conditions (CO2, light, temperature, light quality), molecular mechanisms underlying this potentially adaptive process remain elusive. Herein, we observed that mutants of the circadian rhythm/metabolism factor, Regulator of Phycobilisome Associated A (RpaA), exhibit a striking breakdown of carboxysomes under certain environmental conditions. We find that growth conditions leading to overreduction of the plastoquinone (PQ) pool (mixotrophic growth, high irradiance, or chemical inhibition of electron transfer from PQ to the cytochrome b6f complex) are accompanied by elevated generation of reactive oxygen species (ROS), and correlate with carboxysome breakdown. Carboxysome breakdown is reversed by environmental conditions or chemical inhibitors that prevent PQ overreduction and accompanying ROS generation. Taken together, our data supports a novel link between the redox status of the PQ pool and carboxysome status and/or integrity. Our results have implications for fundamental understanding of cyanobacterial energy balancing pathways and may indicate new research directions for understanding how the carboxysome is remodeled in response to changing environments.

synthetic biology↗

bioRxiv2024

PGR5 is needed for redox-dependent regulation of ATP synthase both in chloroplasts and in cyanobacteria

The regulation of proton motive force (pmf) via ATP synthase activity is a critical mechanism by which photosynthetic organisms maintain redox homeostasis and activate photoprotective responses under fluctuating light conditions. Here, we used time-resolved electrochromic shift (ECS) measurements to investigate pmf dynamics across a range of photosynthetic organisms. Our results reveal that ATP synthase is dynamically regulated during light fluctuations, but in Arabidopsis thaliana could this regulation could not be explained by the known light-induced reduction of the CF{square}{gamma} subunit, suggesting alternative control mechanisms. The PROTON GRADIENT REGULATION 5 (PGR5) protein, previously proposed to facilitate cyclic electron transport (CET), also has a potential role in ATP synthase regulation. The physiological role of cyanobacterial Pgr5 has remained elusive. We characterised a {Delta}pgr5 mutant of Synechocystis sp. PCC 6803 and investigated pmf dynamics in pgr5 mutants of Chlamydomonas reinhardtii, Arabidopsis, and the C4 grass Setaria viridis. While PGR5 was not required for CET in Synechocystis, it was needed for downregulating ATP synthase under high irradiance in all tested organisms via a thiol redox state dependent mechanism. Furthermore, interaction between AtPGR5 and AtCF{square}{gamma} suggests that PGR5 functions as a conserved inhibitor of ATP synthase under high light, contributing to pmf retention and photoprotection. HighlightPGR5 is involved in regulation of ATP synthase in fluctuating light conditions across photosynthetic organisms in a manner that depends on the thiol redox state of the chloroplast or cell.

plant biology↗

bioRxiv2024

The role of the LysR-type transcription factor PacR in regulating nitrogen metabolism in Anabaena sp. PCC7120

In the filamentous model cyanobacterium Anabaena sp. PCC 7120 heterocyst formation is triggered by changes in the C/N-ratio and relies on transcriptional reprogramming in cells. The transcription factor PacR is thought to serve as a global regulator of carbon assimilation under photoautotrophic conditions. In response to Ci-availability, PacR may modulate the carbon concentrating mechanism and photosynthesis, balancing reducing power generation while protecting the photosynthetic apparatus from oxidative damage. However, PacR also binds to promoters of genes associated with heterocyst formation, although the underlying mechanisms remain unclear. To explore this, we studied a response of a PacR-deletion mutant to a nitrogen source shift from ammonium to nitrate. The absence of PacR led to the heterocyst formation in nitrate containing media, as well as reduced growth and chlorophyll-content. We observed impaired nitrate uptake and disrupted ammonium assimilation via the GOGAT-cycle. This phenotype may be exacerbated by reduced PSI-yield and reduced expression of ferredoxin, which may lead to less reducing equivalents for nitrogen assimilation. Our results provide insights into the regulation of heterocyst-formation in Anabaena, potentially advancing its use in biotechnological applications that utilize heterocyst as microoxic cell factories for N2-fixation and hydrogen production.

plant biology↗

bioRxiv2024

Strong heterologous electron sink outcompetes alternative electron transport pathways in photosynthesis

Improvement of photosynthesis requires a thorough understanding of electron partitioning under both natural and strong electron sink conditions. We applied a wide array of state-of-the-art biophysical and biochemical techniques to thoroughly investigate the fate of photosynthetic electrons in the engineered cyanobacterium Synechocystis sp. PCC 6803, a blueprint for photosynthetic biotechnology, expressing the heterologous gene for ene-reductase, YqjM. This recombinant enzyme catalyses the reduction of an exogenously added substrate into the desired product by utilising photosynthetically produced NAD(P)H, enabling whole-cell biotransformation. Through coupling the biotransformation reaction with biophysical measurements, we demonstrated that the strong artificial electron sink, outcompetes the natural electron valves, the flavodiiron protein-driven Mehler-like reaction, and cyclic electron transport. These results show that ferredoxin-NAD(P)H-oxidoreductase (FNR) is the preferred route for delivering photosynthetic electrons from reduced ferredoxin and the cellular NADPH/NADP+ ratio as a key factor in orchestrating photosynthetic electron flux. These insights are crucial for understanding molecular mechanisms of photosynthetic electron transport and harnessing photosynthesis for sustainable bioproduction by engineering the cellular source/sink balance. Furthermore, we conclude that identifying the bioenergetic bottleneck of a heterologous electron sink is a crucial prerequisite for targeted engineering of photosynthetic biotransformation platforms. Significance statementWe coupled the photosynthetic and biocatalytic (whole-cell biotransformation) performance of model cyanobacteria. We employed a heterologous NAD(P)H utilising enzyme, as a strong artificial electron sink, allowing us to gain a comprehensive understanding of photosynthetic electron partitioning. We demonstrated that the strong electron sink outcompetes natural electron sinks and cyclic electron transport.

plant biology↗

bioRxiv2023

Optoelectronic enhancement of photocurrent by cyanobacteria on sustainable AP-VPP-fabricated PEDOT electrodes

Photosynthetic microrganisms, including cyanobacteria, can be interfaced with electrodes in biophotovoltaic devices (BPVs) for solar energy conversion. Effective BPV electrodes need to be conductive, transparent, flexible, biocompatible and environmentally friendly, while also being cost-effective, abundant in material and lightweight. The utilization of electrically conducting polymers (CPs), particularly poly(3,4-ethylenedioxythiophene) (PEDOT) fabricated by an atmospheric pressure vapor phase polymerization (AP-VPP) technique, is a promising avenue for BPV applications. However, challenges remain in optimising their performance as CPs are dynamic optoelectronic materials, and their interaction with photosynthetic biocatalysts under a range of conditions has not been explored thoroughly. Here we show that AP-VPP-PEDOT electrodes hold promise for interfacing with cyanobacteria in BPVs to generate green electricity under red and blue light and moderate applied potentials with exogenous electron mediators. The highest non-mediated photocurrent achieved was 0.48 {micro}A cm-2, with a two-layer PEDOT electrode at 0.5 V applied potential and blue light. The highest mediated photocurrent achieved was 2.73 {micro}A cm-2, with a one-layer PEDOT electrode at 0.3 V applied potential and blue light and the exogenous electron mediator 2,6-dichloro-1,4-benzoquinone (DCBQ). The proposed approach to fabricating PEDOT electrodes offers a new pathway for developing sustainable electrodes for BPVs and pinpoints strategies for future optimisation for achieving high-performance outcomes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/561827v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1af7bfaorg.highwire.dtl.DTLVardef@1f4870forg.highwire.dtl.DTLVardef@cf0b9dorg.highwire.dtl.DTLVardef@1037f31_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2023

Proton motive force dissipation drives flavodiiron proteins to the thylakoid membrane for ferredoxin-powered O2 photoreduction

Flavodiiron proteins (FDPs) catalyse light-dependent reduction of oxygen to water in photosynthetic organisms, creating an electron sink on the acceptor side of Photosystem I that protects the photosynthetic apparatus. However, the identity of the electron donor(s) and the molecular mechanisms regulating FDP activity have remained elusive. To elucidate these issues, we employed spectroscopic and gas flux analysis of photosynthetic electron transport, bimolecular fluorescence complementation assays for in vivo protein-protein interactions in the model cyanobacterium Synechocystis sp. PCC 6803, as well as in silico surface charge modelling. We demonstrated that Ferredoxin-1 interacts with Flv1, Flv2, and Flv3, and is the main electron donor to FDP heterooligomers, which are responsible for the photoreduction of oxygen. Moreover, we revealed that association of FDP heterooligomers with thylakoid membranes is promoted by dissipation of the trans-thylakoid proton motive force, providing the first in vivo evidence of a self-regulatory feedback mechanism allowing dynamic control of FDP activity and maintenance of photosynthetic redox balance in fluctuating environments. Our findings have direct implications for rationally directing electron flux toward desired reactions in biotechnological applications.

plant biology↗

bioRxiv2023

Molecular mechanisms of heavy metal adaptation of an extremophilic red alga Cyanidioschyzon merolae

The order of Cyanidiales comprise seven acido-thermophilic red microalgal species thriving in hot springs of volcanic origin characterized by extremely low pH, moderately high temperatures and the presence of elevated concentrations of sulphites and heavy metals that are prohibitive for most other organisms. Little is known about the molecular mechanisms of Cyanidiales long-term adaptation to such hostile environments, in particular to heavy metals, yet elucidation of these processes is important for understanding the evolution of the metabolic pathways underlying heavy metal detoxification for developing rational strategies for heavy metal bioremediation. Here, we investigated the long-term adaptive responses of Cyanidioschyzon merolae cells, a member of Cyanidiales, to extremely high nickel concentrations. Through complementary approaches based on physiological, microscopic and elemental analyses we dissect several molecular mechanisms underlying the long-term adaptation of this model extremophilic microalga to high Ni exposure. These include: (i) extrusion of Ni from the cells and lack of significant Ni accumulation inside the cells; (ii) maintenance of efficient photoprotective responses including non-photochemical quenching and state transitions; (iii) dynamic remodeling of the chloroplast ultrastructure such as formation of metabolically active prolamellar bodies and plastoglobuli together with loosening of the thylakoid membranes; (iv) activation of ROS amelioration metabolic pathways; and (v) preservation of the efficient respiratory chain functionality. All the dynamically regulated processes identified in this study underlie the remarkable adaptability of C. merolae to extremely high Ni levels that exceed by several orders of magnitude the levels of this heavy metal found in the natural environment of this extremophile.

cell biology↗

bioRxiv2021

Flv3A facilitates O2 photoreduction and affects H2 photoproduction independently of Flv1A in diazotrophic Anabaena filaments

The model heterocyst-forming filamentous cyanobacterium, Anabaena sp. PCC 7120 (Anabaena) represents multicellular organisms capable of simultaneously performing oxygenic photosynthesis in vegetative cells and the O2-sensitive N2-fixation inside the heterocysts. The flavodiiron proteins (FDPs) have been shown to participate in photoprotection of photosynthesis by driving excess electrons to O2 (Mehler-like reaction). Here, we addressed the physiological relevance of the vegetative cell-specific Flv1A and Flv3A on the bioenergetic processes occurring in diazotrophic Anabaena under variable CO2. We demonstrate that both Flv1A and Flv3A are required for proper induction of the Mehler-like reaction upon a sudden increase in light intensity, which is likely important for the activation of carbon-concentrating mechanisms (CCM) and CO2 fixation. Under ambient CO2 diazotrophic conditions, Flv3A is capable of mediating moderate O2 photoreduction, independently of Flv1A, but in coordination with Flv2 and Flv4. Strikingly, the lack of Flv3A resulted in strong downregulation of the heterocyst-specific uptake hydrogenase, which led to enhanced H2 photoproduction under both oxic and micro-oxic conditions. These results reveal a novel regulatory network between the Mehler-like reaction and the diazotrophic metabolism, which is of great interest for future biotechnological applications.

plant biology↗

bioRxiv2019

Flavodiiron proteins and NDH-1 cooperate to maintain photosynthetic redox poise in Synechocystis

In oxygenic photosynthetic organisms excluding angiosperms, flavodiiron proteins (FDPs) catalyze light-dependent reduction of O2 to H2O. This alleviates electron pressure on the photosynthetic apparatus and protects it from photodamage. In Synechocystis sp. PCC 6803, four FDP isoforms function as hetero-oligomers of Flv1 and Flv3 and/or Flv2 and Flv4. An alternative electron transport pathway mediated by the NAD(P)H dehydrogenase-like complex (NDH-1) also contributes to redox hemostasis and the photoprotection of photosynthesis. Four NDH-1 types haven been characterized in cyanobacteria: NDH-11 and NDH-12, which function in respiration; and NDH-13 and NDH-14, which function in CO2 uptake. All four types are involved in cyclic electron transport. Along with single FDP mutants ({Delta}flv1 and {Delta}flv3) and the double NDH-1 mutants ({Delta}d1d2, which is deficient in NDH-11,2 and {Delta}d3d4, which is deficient in NDH-13,4), we studied triple mutants lacking either one of Flv1 or Flv3, and NDH-11,2 or NDH-13,4. We show that the presence of either Flv1/3 or NDH-11,2, but not NDH-13,4, is indispensable for survival during changes in growth conditions from high CO2 /moderate light to low CO2 / high light. Our results suggest functional redundancy and crosstalk between FDPs and NDH-11,2 under the studied conditions, and demonstrate that the functions of FDPs and NDH-11,2 are dynamically coordinated for the efficient oxidation of PSI and for photoprotection under variable CO2 and light availability. One sentence summaryFlavodiiron proteins and NDH-1 complex ensure survival of cyanobacterial cells by cooperatively safeguarding the photosynthetic apparatus against excessive reduction

plant biology↗

bioRxiv2019

Cytochrome cM downscales photosynthesis under photomixotrophy in Synechocystis sp. PCC 6803

Photomixotrophy is a metabolic state, which enables photosynthetic microorganisms to simultaneously perform photosynthesis and metabolism of imported organic carbon substrates. This process is complicated in cyanobacteria, since many, including Synechocystis sp. PCC 6803, conduct photosynthesis and respiration in an interlinked thylakoid membrane electron transport chain. Under photomixotrophy, the cell must therefore tightly regulate electron fluxes from photosynthetic and respiratory complexes. In this study, we show via characterization of photosynthetic apparatus and the proteome, that photomixotrophic growth results in a gradual reduction of the plastoquinone pool in wild-type Synechocystis, which fully downscales photosynthesis over three days of growth. This process is circumvented by deleting the gene encoding cytochrome cM (CytM), a cryptic c-type heme protein widespread in cyanobacteria. {Delta}CytM maintained active photosynthesis over the three day period, demonstrated by high photosynthetic O2 and CO2 fluxes and effective yields of Photosystem II and Photosystem I. Overall, this resulted in a higher growth rate than wild-type, which was maintained by accumulation of proteins involved in phosphate and metal uptake, and cofactor biosynthetic enzymes. While the exact role of CytM has not been determined, a mutant deficient in the thylakoid-localised respiratory terminal oxidases and CytM ({Delta}Cox/Cyd/CytM) displayed a similar phenotype under photomixotrophy to {Delta}CytM, demonstrating that CytM is not transferring electrons to these complexes, which has previously been suggested. In summary, the obtained data suggests that CytM may have a regulatory role in photomixotrophy by reducing the photosynthetic capacity of cells. One sentence summaryThe cryptic, highly conserved cytochrome cM completely blocks photosynthesis in Synechocystis under three days of photomixotrophy, possibly by suppressing CO2 assimilation.

plant biology↗