Biology subjects

Bandara, S.

Publications and source records attributed to Bandara, S..

9 recordsLinked to original sources

bioRxiv2026

Crystal structures of a far-red photoreceptor in different light-absorbing states: insights into spectral tuning and light signaling

Cyanobacteriochromes (CBCRs) are bilin-binding photoreceptors with remarkable spectral versatility. Using phycocyanobilin (PCB) as a chromophore, CBCRs regulate diverse light-dependent processes in cyanobacteria, ranging from photosynthesis to chromatic acclimation. Although extensive studies have uncovered multiple spectral tuning mechanisms in bilin-binding proteins, recent structural studies of far-red CBCRs suggest the existence of additional tuning strategies in both the 15Z and 15E states. Here we report crystal structures of the representative far-red CBCR Anacy_2551g3 in three distinct light-absorbing states, all of which adopt a compact all-syn PCB conformation. These structures demonstrate that 15Z/15E photoisomerization in Anacy_2551g3 involves minimal chromophore rotation relative to the GAF domain, in stark contrast to other characterized bilin-based photoreceptors. To investigate the molecular basis of its far-red absorption, we examined the protonation and tautomeric states of PCB in the Pfr state using resonance Raman (RR) spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. Comparisons of experimental and calculated RR spectra support a bilin lactam as the predominant tautomeric form in the Pfr state. Integrating structural, spectroscopic, computational and mutational analyses, we propose that specific protein-chromophore interactions play critical roles in modulating chromophore conjugation beyond bilin coplanarity. Structural analyses further suggest a signaling model in which light regulation by Anacy_2551g3 is mediated through reversible switching between a high-affinity Pfr state and a low-affinity Po state that does not involve large chromophore motions. Together, these results provide new insights into how protein-chromophore coupling governs spectral tuning and light signaling in bilin-based photoreceptors. Significance statementBilins are widespread biological pigments that mediate photoreception, light harvesting, and photosynthesis across diverse light environments. In a phenomenon known as spectral tuning, the optical properties of bilin-binding proteins are profoundly influenced by protein-chromophore interactions. Mechanistic understanding of spectral tuning and light signaling is important not only for advancing fundamental knowledge of light-sensitive proteins but also for developing new engineering strategies in synthetic biology and biotechnology. Recently discovered cyanobacteriochromes (CBCRs) exhibit remarkable spectral diversity and structural versatility, providing excellent model systems for dissecting the mechanisms of bilin-based photoreceptors. By integrating crystallography, spectroscopy and computational methods, this work examines three distinct light absorbing states of a representative far-red CBCR. Our findings reveal previously unrecognized mechanisms of spectral tuning and light signaling, highlighting the critical roles of protein-chromophore coupling and electrostatic interactions in regulating photoreceptor function.

biochemistry↗

bioRxiv2025

Adaptive Disruption of Carotenoid Metabolism in Cavefish via Loss of Beta-carotene oxygenase 2a (Bco2a)

Vitamin A is an essential micronutrient that supports vision, immunity, and development, yet excess vitamin A can be toxic1,2. Most vertebrates maintain tightly regulated vitamin A levels by cleaving dietary carotenoids into retinoids via specialized enzymes, including the mitochondrial carotenoid oxygenase Bco23,4. To what extent genetic changes in carotenoid-metabolism enzymes like Bco2 drive natural variation in vitamin A homeostasis remains unclear. Here we show that multiple cave-adapted populations of the Mexican tetra (Astyanax mexicanus) have evolved loss-of-function mutations in bco2a, leading to impaired carotenoid cleavage and dramatic carotenoid and vitamin A accumulation. These mutations yield enzymatically inactive Bco2a proteins, are under selection in cavefish, and may provide a physiological advantage under inconsistent carotenoid supply. Contrary to expectations from mammalian models where Bco2 loss induces oxidative damage5,6, cavefish appear to tolerate and even benefit from carotenoid accumulation, potentially through enhanced antioxidant capacity and modified mitochondrial metabolism. Our findings reveal that the vitamin A regulatory system is evolutionarily flexible, and that the adaptive loss of Bco2a function may enable survival in nutrient-variable, low-oxygen cave environments. This work provides a framework for understanding how animals balance essential nutrient thresholds in extreme environments.

evolutionary biology↗

bioRxiv2025

Retinoic acid production via the ray-finned fish gene beta-carotene oxygenase 1-like is essential for juvenile development

In vertebrates, vitamin A (VA) is crucial for development, tissue homeostasis, vision, and immunity. Retinal, a form of VA, is produced via enzymatic cleavage of {beta}-carotene by beta-carotene oxygenase 1 (bco1) and bco1-like (bco1l). While bco1 is found across vertebrate taxa, bco1l is a paralog of bco1 that we discover to have evolved in the ray-finned fishes, the most abundant, speciose, and commercially important group of fishes. We investigated the function of bco1l in ray-finned Siamese fighting fish, commonly known as betta, an emerging model for genetics and development. Using CRISPR-Cas9 knockouts, we find that lack of bco1l results in reduced VA and elevated {beta}-carotene in larvae, starting when animals have exhausted their yolk supply of retinal, followed by stunted growth and death during juvenile development. Exogenous retinoic acid rescues the mutation, demonstrating its deficiency causes these defects. bco1l is 4x more abundant than bco1 in the intestine. This, coupled with the inability of bco1 to sustain VA production in the bco1l mutant, indicates that bco1l is the primary enzyme for dietary carotenoid conversion into retinal. Our results show that VA production by bco1l is required for post-embryonic development, and that bco1l became essential after evolving via duplication of bco1.

genetics↗

bioRxiv2024

The Plasmodium falciparum NCR1 membrane protein is a novel antimalarial target that exports cholesterol to maintain membrane homeostasis

Malaria is an extremely devastating parasitic infection that kills over half a million people each year. It is the leading cause of death in many developing countries, in part, due to a lack of resources and readily available therapeutics. Unfortunately, the most prevalent and deadliest causative agent of malaria, Plasmodium falciparum, has developed resistance to nearly all currently available antimalarial drugs. The P. falciparum Niemann-Pick Type C1-related (PfNCR1) transporter has been identified as a druggable target, as it is required for membrane homeostasis of the parasite. However, the structure and detailed molecular mechanism of this membrane protein are not yet available. Here we present three structures of PfNCR1 both in the absence and presence of the functional inhibitor MMV009108 at resolutions between 2.98 [A] and 3.81 [A] using single-particle cryo-electron microscopy (cryo-EM). The data suggest that PfNCR1 binds cholesterol and forms a cholesterol transport tunnel to modulate the composition of the parasite plasma membrane. Cholesterol efflux assays substantiate this as they show that PfNCR1 is an exporter capable of extruding cholesterol from the membrane. Additionally, the inhibition mechanism of MMV009108 appears to be due to a direct blockage of PfNCR1, preventing this transporter from shuttling cholesterol.

biochemistry↗

bioRxiv2023

Use of nanomaterials-modified carbon microfiber electrode material for superior electrochemical performance in lake sediment inoculated microbial fuel cells

High cathodic overpotential of the oxygen reduction reaction (ORR) in MFC carbon-based cathodes is one of the key barriers to the widespread adoption of the technology. Current Pt-based ORR catalysts are expensive. The use of novel and inexpensive catalysts as replacements for platinum is therefore desirable. In this study, nanomaterials were directly chemically synthesized on carbon microfiber electrodes to improve the performance of lake sediment inoculated MFCs. Nanomaterial of MnO2, MnO2/polyaniline (PANI), ZnO/NiO and ZnO/NiO/PANI attachments were directly chemically synthesized on the carbon material and used as cathode electrodes. The maximum power densities recorded for the different treatments were; MnO2 78.5 mW/m2, MnO2/PANI (Polyaniline) 141.6 mW/m2, ZnO/NiO 67.6 mW/m2, and ZnO/NiO/PANI 129.4 mW/m2. The current and poswer densities were more than six-fold higher in ZnO/NiO/PANI and MnO2/PANI nanoparticle modified cathodes compared to the control MFCs with no catalyst. Cyclic voltammetry (CV) and FTIR data and SEM images suggest that the nanoparticle attached carbon material is morphologically, chemically and electrochemically different from the controls with no nanomaterial attachment. The outcome of this study demonstrates that nanomaterials-incorporated carbon microfiber cathodes bring about significant enhancements to power densities and may potentially have applications in cost-effective MFCs.

bioengineering↗

bioRxiv2022

The use of Statin-class compounds to suppress methanogenesis in lake sediment inoculated microbial fuel cells

Methanogenesis conducted by archaea acts as a competing metabolic pathway that diverts available carbon and electrons away from exo-electrogenic metabolism in mixed culture inoculated microbial fuel cells (MFCs). Statin-class compounds are known to selectively inhibit eukaryotic and archaeal versions of HMG Co-A reductase (class-I) enzyme and the bacterial version of the same enzyme (class-II) is known to be unresponsive to statins. The results of this study demonstrated that the two model statin compounds Simvastatin and Atorvastatin were effective in suppressing methanogenesis in MFCs when applied in moderate concentrations (5 mg/L and 40 mg/L respectively) in MFC anodes. Power densities increased 2 fold compared to control (to 63 {+/-} 1.8 mW/m2) and 2.5 fold (to 69.5 {+/-} 1.8 mW/m2) with Simvastatin and Atorvastatin addition respectively. There was an almost complete suppression of CH4 production with the addition of both statins into MFC anodes as shown by gas composition analysis. Quantitative FISH (qFISH) analysis showed that methanogens Methanosarcina, Metanobacteria and Methanomicrobiales together with all archaea were almost completely suppressed when statins were supplemented into MFC anodes. This study demonstrated that the statins addition can be used to boost power densities in MFCs.

microbiology↗

bioRxiv2021

Genomic consequences of domestication of the Siamese fighting fish

Siamese fighting fish, commonly known as betta, are among the worlds most popular and morphologically diverse pet fish, but the genetic processes leading to their domestication and phenotypic diversification are largely unknown. We assembled de novo the genome of a wild Betta splendens and whole-genome sequenced multiple individuals across five species within the B. splendens species complex, including wild populations and domesticated ornamental betta. Given our estimate of the mutation rate from pedigrees, our analyses suggest that betta were domesticated at least 1,000 years ago, centuries earlier than previously thought. Ornamental betta individuals have variable contributions from other Betta species and have also introgressed into wild populations of those species. We identify dmrt1 as the main sex determination gene in ornamental betta but not in wild B. splendens, and find evidence for recent directional selection at the X-allele of the locus. Furthermore, we find genes with signatures of recent, strong selection that have large effects on color in specific parts of the body, or the shape of individual fins, and are almost all unlinked. Our results demonstrate how simple genetic architectures paired with anatomical modularity can lead to vast phenotypic diversity generated during animal domestication, and set the stage for using betta as a modern system for evolutionary genetics. One-Sentence SummaryGenomic analyses reveal betta fish were domesticated more than 1,000 years ago and the genes that changed in the process.

evolutionary biology↗

bioRxiv2020

Molecular Basis of Far-red Sensing in Cyanobacteriochrome

Cyanobacteriochromes are small, panchromatic photoreceptors in the phytochrome superfamily that regulate diverse light-mediated adaptive processes in cyanobacteria. The molecular basis of far-red (FR) light perception by cyanobacteriochromes is currently unknown. Here we report the crystal structure of a far-red-sensing cyanobacteriochrome from Anabaena cylindrica PCC 7122, which exhibits a reversible far-red/orange photocycle. The 2.7 [A] structure of its FR-absorbing dark state, determined by room temperature serial crystallography and cryo-crystallography, reveals an all-Z,syn configuration of its bound linear tetrapyrrole (bilin) chromophore that is less extended than the bilin chromophores of all known phytochromes. Based on structural comparisons with other bilin-binding proteins and extensive spectral analyses on mutants, we identify key protein-chromophore interactions that enable far-red sensing in bilin-binding proteins. We propose that FR-CBCRs employ two distinct tuning mechanisms, which work together to produce a large batho-chromatic shift. Findings of this work have important implications for development and improvement of photoproteins with far-red absorption and fluorescence. Significance StatementPhytochromes are well known far-red-light sensors found in plants that trigger adaptive responses to facilitate competition for light capture with neighboring plants. Red- and far-red-sensing are critical to cyanobacteria living in the far-red-enriched shade of plants. Here we report the crystal structure of a far-red-sensing cyanobacteriochrome, a distant cyanobacterial relative of phytochrome. These studies shed insight into the poorly understood molecular basis of far-red-sensing by phytobilin-based photoreceptors. Owing to the deep tissue penetration of far-red light, far-red-sensing photoreceptors offer promising protein scaffolds for developing gene-based photoswitches, optoacoustic contrast agents and fluorescent probes for in situ imaging and optogenetic applications.

biochemistry↗

bioRxiv2020

Genetic Distance Calculation Based on Locality Sensitive Hashing

Measuring the genetic relatedness between different species is one of the major challenges in the field of phylogenetics. Genetic distance calculation based on DNA data is highly using a mechanism to determine inter species relationships. Genetic distance computation can be further bifurcated as alignment-free sequencing and alignment based sequencing. With this research we are presenting alignment free genetic distance calculation technique which is based on locality sensitive hashing(LSH). By this approach we are hashing large DNA sequences into numeric arrays and make comparison more efficient and simplified.

bioinformatics↗