Biology subjects

Hirose, Y.

Publications and source records attributed to Hirose, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Dynamic evolution of diaphorin biosynthetic genes against a background of genome conservation in Profftella

The Asian citrus psyllid Diaphorina citri (Insecta: Hemiptera), a major agricultural pest, harbors the unusual obligate bacterial symbiont "Candidatus Profftella armatura" (Profftella), which is intimately integrated with its host yet devotes a remarkably large proportion of its highly reduced genome to the production of diaphorin, a bioactive polyketide. To gain insight into the evolution of this distinctive symbiont, we determined the genomes of Profftella and the co-resident nutritional symbiont "Candidatus Carsonella ruddii" (Carsonella) from Diaphorina lycii and compared them with previously characterized counterparts from D. citri and D. cf. continua. The Profftella and Carsonella chromosomes from D. lycii were 471 and 174 kb, respectively, and Profftella harbored an 8-kb plasmid. Genome organization and gene content were highly conserved across the three lineages. The diaphorin biosynthetic system likewise retained its overall organization, consistent with an important role for diaphorin in the Diaphorina symbiotic system. Remarkably, however, pronounced lineage-specific structural variation was observed in diaphorin synthases DipP and DipT, encoded by two of the 20 diaphorin biosynthetic genes. These synthases contained three extensively amplified tandem arrays of acyl carrier protein (ACP) domains that carry growing polyketide intermediates, with up to seven copies compared with one or two at corresponding positions in the related pederin synthases. All three regions of tandem ACP repeats showed copy-number variation among the Profftella lineages. This variation indicates that ACP amplification remains evolutionarily dynamic despite the otherwise highly constrained symbiotic genome. Together, our findings show that even highly integrated obligate symbionts retain evolutionary flexibility in specialized functional systems.

genomics↗

bioRxiv2026

Diaphorin induces extensive transcriptional remodeling of translation, transport, metabolism, and stress responses in Escherichia coli

Diaphorin is a pederin-family polyketide produced by the obligate bacterial symbiont "Candidatus Profftella armatura" (Betaproteobacteria) of the Asian citrus psyllid Diaphorina citri, in which it accumulates at millimolar concentrations. Diaphorin suppresses the growth of many bacterial species but promotes the growth and metabolic activity of Escherichia coli, highlighting the importance of elucidating the mechanisms underlying these contrasting effects. Although cell-free studies show that diaphorin directly affects bacterial translation, how E. coli transcription changes during growth promotion remains unclear. Here, we analyzed the transcriptome of E. coli after 7 h of exposure to 5 mM diaphorin, when its growth-promoting effect is most pronounced. Diaphorin altered the expression of 1,278 of 4,269 analyzed genes. Functional enrichment analyses revealed strong negative enrichment of translation- and ribosome-related functions, pathway-specific changes in metabolism, and enrichment of transport-, stress-response, and quorum-sensing-related functions. Ribosomal protein genes were broadly downregulated, whereas coordinated upregulation was observed in mdtEF, prpBCDE, the Gad system, and luxS/lsr genes. These findings indicate functionally structured transcriptional remodeling during diaphorin-enhanced growth. Together with previous cell-free evidence, the pronounced translation-related changes observed here highlight bacterial translation as a major process associated with the response of E. coli to diaphorin. One possible interpretation of the apparently contrasting observations is that an earlier stimulation of bacterial translation is followed by compensatory downregulation of translation-related genes as growth proceeds. More broadly, these transcriptional changes provide insight into diaphorin-enhanced growth in E. coli and offer a basis for understanding the strikingly different effects of this symbiont-derived polyketide among bacterial species.

microbiology↗

bioRxiv2026

Disruption of cAMP Signalling and RNA Regulation Confers Cefiderocol Resistance in Acinetobacter baumannii

Cefiderocol is a siderophore-conjugated cephalosporin used to treat severe multidrug-resistant Gram-negative infections. Its recent prioritisation for US national preparedness underscores its clinical importance, yet resistance can emerge despite apparent in vitro susceptibility. Here, we identify two regulatory routes to cefiderocol resistance in carbapenem-resistant Acinetobacter baumannii (CRAB): mutation of the cAMP-producing adenylate cyclase CavA and truncation of the glycine-rich RNA-binding domain of the post-transcriptional regulator Hfq. These variants occurred in contemporary clinical isolates, conferred resistance in a murine CRAB lung-infection model and imposed minimal fitness costs. In Escherichia coli, deletion of the CavA orthologue cyaA increased competitive fitness during sub-inhibitory cefiderocol exposure. Hfq-CLASH and integrated omics revealed Hfq-dependent regulation of Fur-associated iron homeostasis in A. baumannii. Under iron limitation, truncated-Hfq induced a defence-primed state that attenuated siderophore uptake and reduced cefiderocol activity. These findings identify bacterial regulatory state and iron availability as determinants of cefiderocol susceptibility, with implications for resistance surveillance and susceptibility testing.

microbiology↗

bioRxiv2026

NECTIN4 defines a subtype-dependent tumor state coupling enfortumab vedotin targetability to antitumor immunity in bladder cancer

NECTIN4 is the target of enfortumab vedotin (EV), but its biological role in bladder cancer (BC) and its relationship to EV plus PD-1 blockade remain unclear. Integrating clinical multi-omics, spatial and single-cell immune profiling, and experimental models, we identify NECTIN4 as a subtype-dependent determinant of tumor state and antitumor immunity. In basal BC cells, NECTIN4 suppressed inflammatory and mesenchymal programs. Consistently, NECTIN4-high basal/squamous muscle-invasive BCs showed favorable survival, higher checkpoint inhibitor response rates, and a coordinated CD8+ T cell-inflamed microenvironment with no comparable associations in luminal papillary tumors. In orthotopic models, murine Nectin4 promoted CD8+ T cell-dependent tumor control, whereas human NECTIN4 conferred EV sensitivity. EV also attenuated NECTIN4-dependent TIGIT binding. Conversely, NECTIN4-low models were preferentially sensitive to HDAC inhibition. NECTIN4 therefore couples antibody-drug conjugate targetability to a subtype-specific tumor-immune state permissive for checkpoint blockade, whereas the NECTIN4-low state defines a distinct inflammatory-mesenchymal state with an alternative therapeutic vulnerability.

cancer biology↗

bioRxiv2026

Production of cellobiose from ionic liquid-treated cellulose using the highly thermostable cellobiohydrolase HmCel6A-3SNP at 80°C and analysis of enzymatic accessibility to the substrate

Cellobiose is an important disaccharide used in food, health, and biorefinery applications, but its efficient enzymatic production from crystalline cellulose remains challenging. In this study, crystalline cellulose was dissolved in ionic liquids and regenerated by dilution, and subsequently hydrolyzed at 80{degrees}C using a highly thermostable cellobiohydrolase, HmCel6A-3SNP. The enzyme retained activity in the presence of low concentrations of ionic liquids. Among the pretreatment conditions tested, cellulose treated with 1-butyl-3-methylimidazolium chloride ([Bmim]Cl) showed the highest enzymatic digestibility. After washing to remove residual ionic liquid, the reaction produced reducing sugars at levels 1.5-fold higher than those obtained in the presence of 10% [Bmim]Cl, with cellobiose accounting for approximately 96% of the products. Under the optimized conditions, the hydrolysis yield reached [~]36% after 48 hr. Structural analyses using birefringence imaging, electron microscopy, and Fourier transform infrared spectroscopy indicated that higher-order structural changes in regenerated cellulose strongly influence enzymatic accessibility. These results demonstrate the potential of combining ionic-liquid pretreatment with thermostable enzymes for selective cellobiose production from cellulose.

biochemistry↗

bioRxiv2026

Monounsaturated fatty acid biosynthesis is critical for streptococcal envelope homeostasis and stress tolerance

AbstractThe genus Streptococcus contains some of the most important commensals and pathogens of the human microbiome. To obtain the fatty acids required for cell membranes, Streptococcus either produce fatty acids de novo through the fatty acid biosynthesis (fab) pathway or uptake host fatty acids through the fatty acid kinase (fak) pathway. Although both the fab and fak pathways represent potential therapeutic targets to prevent or treat infection, progress is limited because of an incomplete understanding of taxon-to-taxon variability in streptococcal lipid metabolism. Here, we examined the role of de novo monounsaturated fatty acid (MUFA) synthesis in physiology and virulence-associated traits in Streptococcus mutans, Streptococcus pyogenes, and Streptococcus pneumoniae, three major pathogens that cause disease at distinct body sites. In all three species, deletion of fabM abolished MUFA production and caused severe growth defects, decreased stress tolerance, increased antibiotic susceptibility, and defects in cell viability, morphology, and division. In S. mutans, loss of fabM also markedly reduced competence signaling and production of the mutacin IV bacteriocin. Deletion of fabM increased susceptibility to killing by human neutrophils in S. mutans and S. pneumoniae, but not S. pyogenes. Together, these findings illustrate that MUFA synthesis is broadly important for streptococcal physiology and cell membrane homeostasis, while its contribution to pathogenesis is strongly species- and context-dependent, providing leads to guide development of novel therapeutic and/or preventative strategies.

microbiology↗

bioRxiv2025

Glycerol suppresses lactose-dependent growth of Streptococcus pyogenes through a transcription-independent mechanism

Streptococcus pyogenes (group A Streptococcus; GAS) requires flexible metabolic regulation to adapt to diverse host environments; however, its physiological responses to lactose and glycerol remain poorly characterized compared with glucose. In this study, we analyzed three representative serotype M1 GAS strains--the M1global strain 5448, the ancestral M1 strain SF370, and SP1380 as a representative of the recently emerged M1UK lineage. Glycerol consistently suppressed lactose-dependent growth across all strains, while glycerol-dependent respiratory activity was observed in 5448 and SF370 but was absent in SP1380. RNA-seq analysis of strain 5448 revealed no significant transcriptional changes upon glycerol supplementation, indicating that this inhibitory effect likely occurs through a non-transcriptional mechanism. In contrast, lactose supplementation induced distinct transcriptional programs compared with glucose, including coordinated expression changes gene sets regulated by carbohydrate-responsive transcription factors (CcpA, MalR, and NanR) and by the virulence regulator Mga and the stress-response regulator Rgg. Together, these findings identify a previously unrecognized layer of carbon source-dependent metabolic regulation and growth control in GAS.

microbiology↗

bioRxiv2025

Sexual life cycle establishes the unicellular red algae Cyanidiophyceae as a genetically tractable model lineage for eukaryotic evolution

The thermo-acidophilic unicellular algal class Cyanidiophyceae is the earliest-branching lineage in red algae, which diverged from Viridiplantae lineage (green algae and land plants) soon after chloroplast establishment in the common ancestor of Archaeplastida. Cyanidiophyceae possess extremely simple genomes (8.7-17.8 Mb; approximately 4,800- 7,800 genes), and the cell-wall-less, genetically tractable strain Cyanidioschyzon merolae 10D has served as a model organism. However, its unknown sexual life cycle has limited its utility in studies of evolution and genetics. Inspired by the recent discovery of sexual reproduction in the cyanidiophycean genus Galdieria, we identified similar life cycles in the other cyanidiophycean genera Cyanidioschyzon, Cyanidiococcus, and Cyanidium. In these genera, the cell-walled diploid form, exclusively observed in nature, produces a cell-wall-less haploid form when the culture pH is lowered, and both proliferate asexually. In addition, the cell-wall-less Cyanidioschyzon merolae 10D strain has been shown to be a haploid clone that forms a cell-walled diploid through mating with other haploid clones. Building on these findings, we generated high-quality genomic resources with phase-specific transcriptomes and developed genetic manipulation systems using the cell-wall-less haploids of these genera. We further uncovered phase-specific distribution of histone H3 lysine 27 trimethylation linked to haploid- and diploid-specific gene expression, including transcription factors involved in differentiation associated with sexual reproduction in plants. Additionally, biparental inheritance of organelle DNA occurs following isogamous mating of haploid cells but resolves into uniparental inheritance during diploid proliferation. These advances position Cyanidiophyceae as a powerful model lineage for studying early Archaeplastida evolution, the shared mechanisms of photosynthetic eukaryotes, and their environmental adaptation.

plant biology↗

bioRxiv2024

Identifying Genetic Variations in emm89 Streptococcus pyogenes Linked to Severe Invasive Infections

Streptococcus pyogenes causes mild human infections as well as life-threatening invasive diseases. Since the mutations known to enhance virulence to date account for only half of the severe invasive infections, additional mechanisms/mutations need to be identified. Here, we conducted a genome-wide association study of emm89 S. pyogenes strains to comprehensively identify pathology-related bacterial genetic factors (SNPs, indels, genes, or k-mers). Japanese (n=311) and global (n=666) cohort studies of strains isolated from invasive or non-invasive infections revealed 17 and 1,075 SNPs/indels and 2 and 169 genes, respectively, that displayed associations with invasiveness. We validated one of them, a non-invasiveness-related point mutation, fhuB T218C, by structure predictions and introducing it into a severe invasive strain and confirmed that the mutant showed slower growth in human blood. Thus, we report novel mechanisms that convert emm89 S. pyogenes to an invasive phenotype and a platform for establishing novel treatments and prevention strategies.

microbiology↗

bioRxiv2024

Highly reduced complementary genomes of dual bacterial symbionts in the mulberry psyllid Anomoneura mori

The genomes of obligately host-restricted bacteria suffer from accumulating mildly deleterious mutations, resulting in a drastic size reduction. Psyllids (Hemiptera) are phloem sap-sucking insects with a specialized organ called the bacteriome, which typically harbors two vertically transmitted bacterial symbionts: the primary symbiont "Candidatus Carsonella ruddii" (Gammaproteobacteria) and a secondary symbiont phylogenetically diverse among psyllid lineages. Genomes of several Carsonella lineages were revealed to be drastically reduced (158-174 kb), AT-rich (14.0-17.9% GC), and structurally conserved with similar gene inventories devoted for synthesizing essential amino acids scarce in the phloem sap. However, genomic information for secondary symbionts was limited. Hence, this study analyzed genomes of the bacteriome-associated dual symbionts, Secondary_AM (Gammaproteobacteria) and Carsonella_AM, in the mulberry psyllid Anomoneura mori (Psyllidae). This revealed that the Secondary_AM genome is as small and AT-rich (229,822 bp, 17.3% GC) as those of Carsonella, including Carsonella_AM (169,120 bp, 16.2% GC), implying that Secondary_AM is an evolutionarily ancient obligate mutualist like Carsonella. Phylogenomic analyses demonstrated that Secondary_AM is sister to "Candidatus Psyllophila symbiotica" of Cacopsylla spp. (Psyllidae), whose genomes (221-237 kb, 17.3-18.6% GC) were recently reported. The Secondary_AM and Psyllophila genomes showed highly conserved synteny, sharing all genes for complementing the incomplete tryptophan biosynthetic pathway of Carsonella and genes for synthesizing B vitamins. However, sulfur assimilation and carotenoid synthesizing genes were retained only in Secondary_AM and Psyllophila, respectively, indicating ongoing gene silencing. Average nucleotide identity, gene ortholog similarity, genome-wide synteny, and substitution rates suggested that the Secondary_AM/Psyllophila genomes are more labile than the Carsonella genomes.

genomics↗

bioRxiv2024

Synchronization between chloroplastic and cytosolic protein synthesis for photosynthesis complex assembly

Through symbiosis, subunits of chloroplastic complexes are encoded in distinct genomes in the nucleus and organelles. For plant cells to maintain the stoichiometry of subunits and respond to environmental cues, the orchestration of the nuclear and organellar gene expression systems is an essential task. However, the mechanism maintaining chloroplastic complexes remains largely enigmatic. Here, we simultaneously assessed the translatomes of the chloroplast and the cytoplasm via ribosome profiling and revealed the differential mechanisms employed by these two systems to cope with acute light/dark transitions: in chloroplasts, translational regulation is employed, whereas in the cytoplasm, control of the mRNA abundance is implemented. This strategy is widely conserved in land plants (Arabidopsis and the grass plant Brachypodium) and green algae (Chlamydomonas). The translational control in chloroplasts may be established based on organelle symbiosis; the primitive chloroplast in Glaucophyta (Cyanophora) was found to have already acquired translational control, whereas cyanobacteria (Synechocystis) control the mRNA abundance. Moreover, reduced plastoquinones and active cytosolic protein synthesis drive chloroplastic translation of the complex subunits in the light. Our work reveals an early origin of coordination of chloroplast and nuclear/cytoplasmic gene expression upon light exposure.

molecular biology↗

bioRxiv2024

Microbiome of psyllids of the family Aphalaridae, including Aphalara itadori, a potential biocontrol agent against Reynoutria spp.

Several European and North American countries have started releasing the Japanese knotweed psyllid Aphalara itadori (Hemiptera: Aphalaridae) to control the Japanese knotweed Reynoutria japonica (Caryophyllales: Polygonaceae) and its relatives, which are among the worst invasive exotic plants. However, establishing populations of the current Kyushu and Hokkaido strains in the field has not been successful, desiring new lineages. Moreover, little is known about the microbiome of the current strains, which potentially impacts properties as biocontrol agents. Hence, this study analyzed the microbiota of an A. itadori strain newly collected on Honshu Island, along with related species of the family Aphalaridae, using amplicon sequencing of 16S rRNA genes. The A. itadori symbionts were further located using fluorescence in situ hybridization. The results demonstrated that the analyzed A. itadori strain has a dual symbiotic system with "Candidatus Carsonella ruddii" (Gammaproteobacteria: Oceanospirillales) and Sodalis sp. (Gammaproteobacteria: Enterobacterales) harbored in the bacteriome, suggesting their evolutionarily stable mutualistic relationships with A. itadori. The central area of the bacteriome harboring Sodalis appeared to comprise uninucleate bacteriocytes with nuclei larger than those of bacteriocytes for Carsonella, rather than a syncytium with smaller nuclei as previously reported for various psyllid lineages. No known plant pathogens or manipulators of insect reproduction were identified in the analyzed strain, indicating its suitability as a biocontrol agent, posing a minimum risk to the ecosystem. Besides distinct Carsonella lineages, the analysis identified Sodalis independently acquired by Craspedolepta miyatakeai, and an ambiguous Enterobacterales symbiont in Epheloscyta kalopanacis. Only Carsonella was identified in Togepsylla matsumurana.

molecular biology↗

bioRxiv2023

Structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs

Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and their structural variety in photosystem I-LHC (PSI-LHCI) supercomplexes has been shown. However, structural and evolutionary correlations of red-lineage LHCs are unknown. Here we determined a 1.92-[A] resolution cryo-electron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137) which is an important taxon in the Cyanidiophyceae, and subsequently investigated these correlations through structural comparisons and phylogenetic analysis. The PSI-LHCI structure shows five LHCI subunits together with a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae, whereas no orthologous relationships were found between C. caldarium Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.

plant biology↗

bioRxiv2022

Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins

Streptococcus pyogenes can cause a wide variety of acute infections throughout the body of its human host. The underlying transcriptional regulatory network (TRN) is responsible for altering the physiological state of the bacterium to adapt to each host environment. Consequently, an in-depth understanding the comprehensive dynamics of its TRN could inform new therapeutic strategies. Here, we compiled 116 existing high-quality RNA-seq data sets of S. pyogenes serotype M1, and estimated the TRN structure in a top-down fashion by performing independent component analysis (ICA). The algorithm computed 42 independently modulated sets of genes (iModulons). Four iModulons contained nga-ifs-slo virulence-related operon, which allowed us to identify carbon sources that control its expression. In particular, dextrin utilization upregulated nga-ifs-slo operon by activation of two-component regulatory system CovRS-related iModulons, and changed bacterial hemolytic activity compared to glucose or maltose utilization. Finally, we show that the iModulon-based TRN structure can be used to simplify interpretation of noisy bacterial transcriptome at the infection site.

microbiology↗

bioRxiv2022

Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for SARS-CoV-2 3CL Protease

The pandemic of coronavirus disease 2019 (COVID-19) has urgently necessitated the development of antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The 3C-like protease (3CLpro) is a promising target for COVID-19 treatment. Here, we report the new class of covalent inhibitors for 3CLpro possessing chlorofluoroacetamide (CFA) as a cysteine reactive warhead. Based on the aza-peptide scaffold, we synthesized the series of CFA derivatives in enantiopure form and evaluated their biochemical efficiencies. The data revealed that 8a (YH-6) with R configuration at the CFA unit strongly blocks the SARS-CoV-2 replication in the infected cells and this potency is comparable to that of nirmatrelvir. The X-ray structural analysis shows that 8a (YH-6) forms a covalent bond with Cys145 at the catalytic center of 3CLpro. The strong antiviral activity and sufficient pharmacokinetics property of 8a (YH-6) suggest its potential as a lead compound for treatment of COVID-19.

biochemistry↗

bioRxiv2022

Diaphorin, a polyketide produced by a bacterial symbiont of the Asian citrus psyllid, inhibits the growth of Bacillus subtilis but promotes the growth of Escherichia coli

Diaphorin is a polyketide produced by Candidatus Profftella armatura (Gammaproteobacteria: Burkholderiales), an obligate symbiont of a notorious agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae). Diaphorin belongs to the pederin family of bioactive agents found in various host-symbiont systems, including beetles, lichens, and sponges, harboring phylogenetically diverse bacterial producers. Previous studies showed that diaphorin has inhibitory effects on various eukaryotes, including the natural enemies of D. citri. However, little is known about its effects on prokaryotic organisms. To address this issue, the present study assessed the biological activities of diaphorin on two model prokaryotes, Escherichia coli (Gammaproteobacteria: Enterobacterales) and Bacillus subtilis (Firmicutes: Bacilli). The analyses revealed that diaphorin inhibits the growth of B. subtilis but moderately promotes the growth of E. coli. This finding implies that diaphorin functions as a defensive agent of the holobiont (host + symbionts) against some bacterial lineages but is beneficial for others, which potentially include obligate symbionts of D. citri. ImportanceCertain secondary metabolites, including antibiotics, evolve to mediate interactions among organisms. These molecules have distinct spectra for microorganisms and are often more effective against Gram-positive bacteria than Gram-negative ones. However, it is rare that a single molecule has completely opposite activities on distinct bacterial lineages. The present study revealed that a secondary metabolite synthesized by an organelle-like bacterial symbiont of psyllids inhibits the growth of Gram-positive Bacillus subtilis but promotes the growth of Gram-negative Escherichia coli. This finding not only provides insights into the evolution of symbiosis between animal hosts and bacteria but may also potentially be exploited to promote the effectiveness of industrial material production by microorganisms.

microbiology↗

bioRxiv2022

An M protein coiled coil unfurls and exposes its hydrophobic core to capture LL-37

Surface-associated, coiled-coil M proteins of Streptococcus pyogenes (Strep A) disable human immunity through interaction with select proteins. However, coiled coils lack features typical of protein-protein interaction sites, and it is therefore challenging to understand how M proteins achieve specific binding, for example, with the human antimicrobial peptide LL-37, leading to its neutralization. The crystal structure of a complex of LL-37 with M87 protein, an antigenic M protein variant from a strain that is an emerging threat, revealed a novel interaction mode. The M87 coiled coil unfurled and asymmetrically exposed its hydrophobic core to capture LL-37. A single LL-37 molecule bound M87 in the crystal, but in solution recruited additional LL-37 molecules, consistent with a protein trap neutralization mechanism. The interaction mode visualized crystallographically was verified to contribute significantly to LL-37 resistance in an M87 Strep A strain, and was identified to be conserved in a number of other M protein types that are prevalent in human populations. Our results provide specific detail for therapeutic inhibition of LL-37 neutralization by M proteins.

microbiology↗

bioRxiv2021

Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome

Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are compositionally and structurally diverse, and exceedingly complex, all of which pose a challenge for a comprehensive understanding of their function. To date, three detailed architectures of PBSs by cryo-electron microscopy (cryo-EM) have been described: a hemiellipsoidal type, a block-type from rhodophytes, and a cyanobacterial hemidiscoidal-type. Here, we report cryo-EM structures of a pentacylindrical allophycocyanin core and phycocyanin-containing rod of a thermophilic cyanobacterial hemidiscoidal PBS. The structures define the spatial arrangement of protein subunits and chromophores, crucial for deciphering the energy transfer mechanism. They reveal how the pentacylindrical core is formed, identify key interactions between linker proteins and the bilin chromophores, and indicate pathways for unidirectional energy transfer.

biochemistry↗