Rubisco Research Articles

Bicarbonate use reduces the photorespiration in Ottelia alismoides adapting to the CO2-fluctuated aquatic systems.

Underwater CO2 concentration fluctuates extremely in natural water bodies. Under low CO2, the unique CO2 concentrating mechanism in aquatic plants, bicarbonate use, can suppress photorespiration. However, it remains unknown (1) to what extent bicarbonate use reduces photorespiration, (2) how exactly photorespiration varies between bicarbonate-users and CO2-obligate users under CO2-fluctuated environments, and (3) what are differences in Rubisco characteristics between these two types of aquatic plants. In the present study, the bicarbonate user Ottelia alismoides and its phylogenetically close CO2-obligate user Blyxa japonica were chosen to answer these questions. The results showed that bicarbonate use saved ~13% carbon loss under low CO2 via decreasing photorespiration in O. alismoides. Through bicarbonate use, the photorespiration of O. alismoides was kept stable both under high and low underwater CO2 concentrations, while the photorespiration significantly increased in the CO2-obligate user B. japonica under low CO2. However, B. japonica showed a significantly higher photosynthesis rate than O. alsimoides when CO2 was sufficient. These differences could be related to the kinetic characteristics of Rubisco showing a higher carboxylation turnover rate (Kcat) in B. japonica, and the similar affinity to CO2 (Kc) and specificity factor (Sc/o) in these two species that might be determined by the variation of six amino acid residuals in Rubisco large subunit sequences, especially the site 281 (A vs. S) and 282 (H vs. F). All these differences in photorespiration and kinetic characteristics of Rubisco could explain the distribution patterns of bicarbonate users and CO2-obligate users in the field.

Reinstatement of the genus Coenobiodiscus for the distinctive colonial diatom Planktoniella muriformis (Bacillariophyta)

Planktonic diatoms of the genus Planktoniella are characterized by organic extensions from the girdle. Planktoniella species are solitary, except for a colonial form that was first described as Coenobiodiscus muriformis from San Diego Bay, California. We established a culture of Planktoniella muriformis from Mazatlán, Gulf of California, in order to solve its phylogenetic affinities using molecular markers. Beyond the distinct colony morphology, P. muriformis has one marginal rimoportula and absence of mantle ribs, while two rimoportulae and numerous mantle ribs are the signature characteristics in the solitary species of the genus Planktoniella. In the SSU-, LSU rRNA and RuBisCO large subunit (rbcL) gene phylogenies, P. muriformis is nested within sequences from the paraphyletic genus Thalassiosira. The sequences are distantly related to the clade of the type species of Planktoniella, P. sol, and four other congeneric species, and the type species of Thalassiosira or any other thalassiosiroid genera, supporting consideration as an independent genus. In the rbcL gene phylogeny, the sequence of P. muriformis allies with distinct thalassiosiroid genera without bootstrap support, while in the SSU and LSU rRNA gene phylogenies it is nested with support as a sister group of two strains of T. hispida or the strain BEN02-35 identified as Thalassiosira angulata, respectively. The considerable genetic distance between these taxa and P. muriformis, and the lack of distinctive common morphological features do not support their placement in the same genus. Based on analyses of nuclear and chloroplast molecular markers, and the distinctive morphology of P. muriformis, with a unique type of colony formation unknown in any other diatom, we reinstate the genus Coenobiodiscus for P. muriformis.

Dynamic photosynthetic labeling and carbon-positional mass spectrometry monitor in vivo Rubisco carbon assimilation rates.

RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (RUBISCO) is the most abundant enzyme and CO2 bio-sequestration system on Earth. Its in vivo activity is usually determined by 14CO2 incorporation into 3-phosphoglycerate (3PGA). However, the radiometric analysis of 3PGA does not distinguish carbon positions. Hence, RUBISCO activity that fixes carbon into the 1-C position of 3PGA and Calvin-Benson-Bassham (CBB) cycle activities that redistribute carbon into its 2-C and 3-C positions are not resolved. This study aims to develop technology that differentiates between these activities. In source fragmentation of gas chromatography-mass spectrometry (GC-MS) enables paired isotopologue distribution analyses of fragmented substructures and the complete metabolite structure. GC-MS measurements after dynamic photosynthetic 13CO2 labelling allowed quantification of the 13C fractional enrichment (E13C) and molar carbon assimilation rates (A13C) at carbon position 1-C of 3PGA by combining E13C from carbon positions 2,3-C2 and 1,2,3-C3 with quantification of 3PGA concentrations. We validated the procedure using two GC-time of flight (TOF)-MS instruments, operated at nominal or high mass resolution, and tested the expected 3PGA positional labelling by in vivo glycolysis of positional labelled glucose isotopomers. Mutant analysis of the highly divergent GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASEs (GAPDH1 and 2) from Synechocystis sp. PCC 6803 revealed full inactivation of the CBB cycle with maintained RUBISCO activity in Δgapdh2 and a CBB cycle modulating role of GAPDH1 under fluctuating CO2 supply. RUBISCO activity in the CBB-deficient Δgapdh2 can re-assimilate CO2 released by catabolic pathways. We suggest that RUBISCO activity in Synechocystis can scavenge carbon lost through the pentose phosphate pathway or other cellular decarboxylation reactions.

Transcriptome Analysis Reveals Key Genes Involved in the Response of Triticum urartu to Boron Toxicity Stress

The domestication and breeding of wheat genotypes through the years has led to the loss in their genetic variation, making them more prone to different abiotic stresses. Boron (B) toxicity is one of the stresses decreasing the wheat cultivars’ yield in arid and semi-arid regions around the world. Wild wheat progenitors, such as Triticum urartu Thumanian ex Gandilyan, possess a broader gene pool that harbors several genes conferring tolerance to various biotic and abiotic stresses. Unfortunately, T. urartu is not well-explored at the molecular level for its tolerance towards B toxicity in soil. In this study, for the first time, we compared the transcriptomic changes in the leaves of a high B-tolerant T. urartu genotype, PI662222, grown in highly toxic B (10 mM B in the form of boric acid) with the ones grown in the control (3.1 μM B) treatment in hydroponic conditions. The obtained results suggest that several mechanisms are involved in regulating the response of the studied T. urartu genotype toward B toxicity. All the growth parameters of T. urartu genotype, including root–shoot length, root fresh weight, and root–shoot dry weight, were less affected by high boron (10 mM) as compared to the boron-tolerant bread wheat cultivar. With a significant differential expression of 654 genes, 441 and 213 genes of T. urartu genotype were down- and upregulated, respectively, in the PI662222 leaves in high B in comparison to the control treatment. While key upregulated genes included those encoding RNA polymerase beta subunit (chloroplast), ATP synthase subunit gamma, chloroplastic, 60S ribosomal protein, and RNA-binding protein 12-like, the main downregulated genes included those encoding photosystem II protein D, ribulose bisphosphate carboxylase small subunit, and peroxidase 2-like. Interestingly, both Gene Ontology enrichment and KEGG pathways emphasized the possible involvement of the genes related to the photosynthetic process and apparatus in the high B tolerance of the T. urartu genotype. The further functional characterization of the identified potential T. urartu genes will facilitate their utilization in crop improvement programs for B toxicity stress.

Drought intensity–responsive changes in photosynthesis‐related proteins, carbohydrate pools and forage quality in Kentucky bluegrass (Poa pratensis L.)

AbstractDrought is a major factor affecting annual forage production and quality. The present study aimed to characterize drought stress–responsive changes in carbohydrate composition and forage quality–related parameters as being linked to the responses of physiological parameters during the regrowth of Kentucky bluegrass (Poa pratensis L.). Drought treatment gradually decreased leaf water potential (Ψw) to a minimum value of −2.94 MPa at day 46. Drought‐responsive increases in H2O2 concentration and lipid peroxidation were significant from day 22 (Ψw = −1.38 MPa), accompanied by the decreased chlorophyll content. Drought stress repressed Rubisco large subunit and several thylakoid membrane protein complexes (PSI, PSII dimer, PSII monomer and cytochrome b6/f). Drought also increased glucose, fructose and sucrose concentrations from day 22. A distinct increase in monosaccharides and disaccharides coincided with a reduction of fructan, especially from day 36 onward, when the enzymatic activity of fructan exohydrolases (1‐FEH and 6‐FEH) became greatly enhanced. Significant changes in forage nutritional parameters also occurred from day 36 (Ψw = −2.74 MPa), as shown by increases in neutral detergent fiber, acid detergent fiber (ADF) and ADF‐lignin with enhanced activity of polyphenol oxidase, as well as a decrease in crude protein content. These drought‐responsive changes in nutritional parameters were strongly correlated with a decrease in in vitro dry matter digestibility (IVDMD). A correlation analysis revealed that drought‐induced accumulation of H2O2 along with decreasing Ψw was closely associated with increases in fiber compounds and ADF‐lignin leading to a decrease in IVDMD. Our results indicate that drought‐responsive reductions in forage quality mainly occurred under severe drought stress (day 36 to day 46, Ψw ≤ −2.74), when H2O2 accumulation and lipid peroxidation were high, were characterized by an accompanied increase in ADF.

Integrated metabolome and transcriptome analyses provide comprehensive insight into dark- and light-responsive mechanisms in Althaea officinalis hairy root cultures

BackgroundLight, an essential factor in plant development, exerts a significant impact on both primary and secondary metabolism in plants. Althaea officinalis, commonly known as marshmallow, offers versatile applications through its leaves and roots. With a plethora of identified bioactive compounds and their extensive use in food, health, and supplements, it is widely cultivated globally. This study aimed to demonstrate the definitive positive impact of dark and light irradiation on both primary and secondary metabolite production in A. officinalis hairy roots and to elucidate the light-responsive mechanism through integrated metabolome and transcriptome analysis.ResultsWhen exposed to light, significant changes with a greenish colour shift were observed in 60 metabolites. Multivariate statistical analysis revealed a distinct separation between light- and dark-treated hairy roots, likely attributed to metabolites such as glutamic acid, phenylalanine, catechin hydrate, and chlorophyll. Correspondingly, the pathways significantly impacted included galactose metabolism, alanine, aspartate, and glutamate metabolism, flavone and flavonol biosynthesis, and phenylalanine metabolism. Light-responsive differentially expressed genes associated with pigment and phenylpropanoid biosynthetic pathways were analysed and compared via RNA sequencing. Furthermore, among the light-related transcription factors, including CONSTANS-LIKE and double B-box zinc finger, which are responsible for photomorphogenic modulation, were upregulated. Moreover, light-responsive genes, such as ribulose bisphosphate carboxylase, photosystem II, and chlorophyll A-B binding family protein, were upregulated.ConclusionsThese findings emphasise that exposure of A. officinalis hairy root culture to light conditions is a useful method for enhancing most of the primary and secondary metabolites.Graphical abstract

Unique biogenesis and kinetics of hornwort Rubiscos revealed by synthetic biology systems

Hornworts are the only land plants that employ a pyrenoid to optimize Rubisco’s CO2 fixation, yet hornwort Rubisco remains poorly characterized. Here we assembled the hornwort Anthoceros agrestis Rubisco (AaRubisco) using the Arabidopsis thaliana SynBio expression system and observed the formation of stalled intermediates, prompting us to develop a new SynBio system with A. agrestis cognate chaperones. We successfully assembled AaRubisco and Rubisco from three other hornwort species. Unlike A. thaliana Rubisco, AaRubisco assembly is not dependent on RbcX or Raf2. Kinetic characterization reveals that hornwort Rubiscos exhibit a range of catalytic rates (3–10 s−1), but with similar affinity (∼30 μM) and specificity (∼70) for CO2. These results suggest that hornwort Rubiscos do not comply with the long-held canonical catalytic trade-off observed in other land plants, providing experimental support that Rubisco kinetics may be phylogenetically constrained. Unexpectedly, we observed a 50% increase in AaRubisco catalytic rates when RbcX was removed from our SynBio system, without any reduction in specificity. Structural biology, biochemistry, and proteomic analysis suggest that subtle differences in Rubisco large-subunit interactions, when RbcX is absent during biogenesis, increases the accessibility of active sites and catalytic turnover rate. Collectively, this study uncovered a previously unknown Rubisco kinetic parameter space and provides a SynBio chassis to expand the survey of other Rubisco kinetics. Our discoveries will contribute to developing new approaches for engineering Rubisco with superior kinetics.

Cathepsin B- and L-like Protease Activities Are Induced During Developmental Barley Leaf Senescence.

Leaf senescence is a developmental process allowing nutrient remobilization to sink organs. Previously cysteine proteases have been found to be highly expressed during leaf senescence in different plant species. Using biochemical and immunoblotting approaches, we characterized developmental senescence of barley (Hordeum vulgare L. var. 'GemCraft') leaves collected from 0 to 6 weeks after the onset of flowering. A decrease in total protein and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunits occurred in parallel with an increase in proteolytic activity measured using the fluorogenic substrates Z-RR-AMC, Z-FR-AMC, and casein labeled with fluorescein isothiocyanate (casein-FITC). Aminopeptidase activity detected with R-AMC peaked at week 3 and then decreased, reaching a low level by week 6. Maximal proteolytic activity with Z-FR-AMC and Z-RR-AMC was detected from pH 4.0 to pH 5.5 and pH 6.5 to pH 7.4, respectively, while two pH optima (pH 3.6 to pH 4.5 and pH 6.5 to pH 7.4) were found for casein-FITC. Compound E-64, an irreversible cysteine protease inhibitor, and CAA0225, a selective cathepsin L inhibitor, effectively inhibited proteolytic activity with IC50 values in the nanomolar range. CA-074, a selective cathepsin B inhibitor, was less potent under the same experimental conditions, with IC50 in the micromolar range. Inhibition by leupeptin and phenylmethylsulfonyl fluoride (PMSF) was weak, and pepstatin A, an inhibitor of aspartic acid proteases, had no effect at the concentrations studied (up to 0.2 mM). Maximal proteolytic activity with the aminopeptidase substrate R-AMC was detected from pH 7.0 to pH 8.0. The pH profile of DCG-04 (a biotinylated activity probe derived from E-64) binding corresponded to that found with Z-FR-AMC, suggesting that the major active proteases are related to cathepsins B and L. Moreover, immunoblotting detected increased levels of barley SAG12 orthologs and aleurain, confirming a possible role of these enzymes in senescing leaves.

A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage

CO2 fixation is commonly limited by inefficiency of the CO2-fixing enzyme Rubisco. Eukaryotic algae concentrate and fix CO2 in phase-separated condensates called pyrenoids, which complete up to one-third of global CO2 fixation. Condensation of Rubisco in pyrenoids is dependent on interaction with disordered linker proteins that show little conservation between species. We developed a sequence-independent bioinformatic pipeline to identify linker proteins in green algae. We report the linker from Chlorella and demonstrate that it binds a conserved site on the Rubisco large subunit. We show that the Chlorella linker phase separates Chlamydomonas Rubisco and that despite their separation by ~800 million years of evolution, the Chlorella linker can support the formation of a functional pyrenoid in Chlamydomonas. This cross-species reactivity extends to plants, with the Chlorella linker able to drive condensation of some native plant Rubiscos in vitro and in planta. Our results represent an exciting frontier for pyrenoid engineering in plants, which is modelled to increase crop yields.

DNA barcoding, pollen and seed characteristics for documentation of four monocot Mediterranean endemic plant species in Egypt

Endemic taxa are critical constituents in the flora of most parts of the world. Recently, most of these taxa have become exposed to extinction. This study aims to increase understanding of four monocot Mediterranean threatened endemic taxa in Egypt (Allium mareoticum Bornm. & Gauba, Bromus aegyptiacus Tausch, Muscari salah-eidii (Täckh. & Boulos) Hosni, Pancratium arabicum Sickenb.) by description of their pollen and seed and authentication of DNA barcoding using rbcL and matK genes. Twenty field visits were conducted from March 2017 till April 2023 including different localities through Mediterranean area for covering the presence of these species. Characterization of pollen grains and seeds were examined using a light (LM) and scanning electron microscopes (SEM). DNA barcoding was carried out for documentation of the four species. Maturase K (matK) and ribulose-bisphosphate carboxylase (rbcL) were used as primers for PCR amplification and gene sequencing. The two genes were successful in identifying Allium mareoticum, Bromus aegyptiacus, and Muscari salah-eidii at the genus level and Pancratium arabicum at both species and genus levels for rbcL marker, and the genus level for matK marker. This study is considered a leading study for new barcodes of (A) mareoticum, (B) aegyptiacus, and M. salah-eidii which were initially made available to the NCBI.

Purification, crystallization, and X-ray crystallographic analysis of ribulose bisphosphate carboxylase large subunit from Hydrogenovibrio marinus

Purification, crystallization, and X-ray crystallographic analysis of ribulose bisphosphate carboxylase large subunit from <i>Hydrogenovibrio marinus</i>

Functional Analysis of the PoSERK-Interacting Protein PorbcL in the Embryogenic Callus Formation of Tree Peony (Paeonia ostii T. Hong et J. X. Zhang).

SERK is a marker gene for early somatic embryogenesis. We screened and functionally verified a SERK-interacting protein to gain insights into tree-peony somatic embryogenesis. Using PoSERK as bait, we identified PorbcL (i.e., the large subunit of Rubisco) as a SERK-interacting protein from a yeast two-hybrid (Y2H) library of cDNA from developing tree-peony somatic embryos. The interaction between PorbcL and PoSERK was verified by Y2H and bimolecular fluorescence complementation analyses. PorbcL encodes a 586-amino-acid acidic non-secreted hydrophobic non-transmembrane protein that is mainly localized in the chloroplast and plasma membrane. PorbcL was highly expressed in tree-peony roots and flowers and was up-regulated during zygotic embryo development. PorbcL overexpression caused the up-regulation of PoSERK (encoding somatic embryogenesis receptor-like kinase), PoAGL15 (encoding agamous-like 15), and PoGPT1 (encoding glucose-6-phosphate translocator), while it caused the down-regulation of PoLEC1 (encoding leafy cotyledon 1) in tree-peony callus. PorbcL overexpression led to increased indole-3-acetic acid (IAA) content but decreasing contents of abscisic acid (ABA) and 6-benzyladenosine (BAPR). The changes in gene expression, high IAA levels, and increased ratio of IAA to ABA, BAPR, 1-Aminocyclopropanecarboxylic acid (ACC), 5-Deoxystrigol (5DS), and brassinolide (BL) promoted embryogenesis. These results provide a foundation for establishing a tree-peony embryogenic callus system.

Two species of the green algae Volvox sect. Volvox from the Japanese ancient lake, Lake Biwa.

Volvox sect. Volvox is a group of green algae with unique morphological features (thick cytoplasmic bridges between somatic cells and spiny zygote walls) and a worldwide distribution. Despite research interest in the diversity of organisms in ancient lakes, Volvox sect. Volvox from ancient lakes worldwide has not been identified to the species level. Here, we established clonal cultures of two species of this group originating from Lake Biwa, an ancient lake in Japan, and performed identification based on morphological and molecular data. One was identified as Volvox kirkiorum based on the nuclear ribosomal DNA internal spacer region (ITS) sequence, bisexual (monoicous or monoecious) spheroids, and zygote morphology. The other showed genetic separation from related species based on the secondary structure of the ITS and results of phylogenetic analysis of a combined data set from the nuclear actin gene, ITS, and two plastid genes (large subunit of RuBisCO and photosystem II CP43 apoprotein gene); it represented a new phylogenetic lineage within Volvox sect. Volvox, suggesting possible endemism in Lake Biwa. This species produced bisexual spheroids with different zygote morphology and zygote number from other species with bisexual spheroids in Volvox sect. Volvox. Therefore, Volvox biwakoensis Nozaki et H. Yamaguchi sp. nov. is described herein. This is the first endemic species of the genus Volvox described from an ancient lake.

Critical stages in pea photosynthesis impaired by tetracycline as an environmental contaminant.

The widespread use of antibiotics in intensive animal husbandry, and the agricultural utilization of manure from such farms, imposes a significant burden on the environment. Consequently, the effects of antibiotics should be studied not only in animals and humans but also in all components of biocenoses and agrocenoses. In our study, we analyze the impact of four different concentrations of tetracycline present in soil (0, 5, 50, and 500mg/kg of soil) on the growth and key photosynthesis parameters of pea seedlings: chlorophyll concentration, aminolevulinic acid concentration, aminolevulinic acid dehydrogenase activity, and ribulose bisphosphate carboxylase-oxygenase (RuBisCO) activity. At the lowest tetracycline concentration, chlorophyll content decreased by 13% compared to the control (0 tetracycline), while at the highest antibiotic concentration, it decreased by as much as 27%. Similarly, the decrease in aminolevulinic acid (a chlorophyll precursor) concentration was significant, amounting to 34%. However, the activity of the dehydrogenase enzyme, which consumes this precursor, decreased even more drastically by 51%, indicating significant disturbances in the light phase of photosynthesis. However, the activity of RuBisCO in pea plants subjected to tetracycline was even more severely affected, dropping by 58%, 69%, and 70% in soils with increasing concentrations of tetracycline. The reduction in enzyme activity could only partially be explained by a less pronounced decrease in the quantity of RuBisCO (large subunit) protein, which amounted to 6.5%, 11%, and 35% for tetracycline concentrations of 5, 50, and 500mg/kg of soil, respectively.

Impact of Molecular Identification of Palm leaves on the preservation and conservation of Palm Leaves-Tala patra Manuscripts

Palm leaves manuscripts preservation is the main target of this research work. Therefore, this research study aimed at molecular identification of palm leaves by DNA Barcoding to assess the potential level on manuscript preservation. This study aims to amplify the rbcL and matK genes in palm leaves collected from different regions of Bangalore. The DNA was isolated by CTAB method and the amplification was done by PCR analysis. DNA barcoding proved to be an efficient tool for proper discrimination of the related species by generating standers that can be used universally. rbcL: A gene found in the chloroplast genome, encoding a large subunit of the enzyme ribulose-bisphosphate carboxylase. matK: Another chloroplast gene coding for maturase K, involved in splicing group II introns. The discrimination is done by accurately sequencing the standard gene region in a very short time (Hebert et al., 2003). rbcL and matK have been having most recommended and vasty studied DNA barcodes for plants, as they are proved by PWG (Pair wise group) to be potential standardized barcodes for plant DNA barcoding. These barcodes are used to properly identify and discriminate any native or foreign plant species (Maloukh et al., 2017). This work guides us the impact/role of molecular identification-DNA Barcoding of palm leaves on the preservation of Palm leaves manuscripts

Composition and temporal dynamics of the phytoplankton community in Laizhou Bay revealed by microscopic observation and rbcL gene sequencing

Laizhou Bay, a major breeding ground for economic marine organisms in the northern waters of China, is facing rapid environmental degradation. In this study, field surveys in this area were conducted in the spring, summer, and autumn of 2020. Microscopic observation and RuBisCO large subunit (rbcL) gene analysis were employed to understand the community structure and temporal dynamics of phytoplankton. The phytoplankton community structures detected by the two methods showed significant differences. Microscopic observation revealed the dominance of dinoflagellates in spring that shifted to the dominance of diatoms in summer and autumn. However, rbcL gene sequencing consistently identified diatoms as dominant throughout all three seasons, with their relative abundance showing an increasing trend. Conversely, the relative abundance of the second- and third-most abundant taxa, namely, haptophytes and ochrophytes, decreased as the seasons transitioned. rbcL gene sequencing annotated more species than microscopy. It could detect haptophytes and cryptophytes, which were overlooked by microscopy. In addition, rbcL gene sequencing detected a remarkable amount of Thalassiosira profunda, which was previously unidentified in this sea area. However, it appeared to underestimate the contribution of dinoflagellates considerably, with most taxa being only identified through microscopic identification. The two methods jointly identified 28 harmful algal bloom taxa with similar detection quantities but substantial differences in species composition. Phytoplankton communities were influenced by temperature, salinity, and nutrients. The results of this work suggest that a combination of multiple techniques is necessary for a comprehensive understanding of phytoplankton.

The chloroplast pentatricopeptide repeat protein RCN22 regulates tiller number in rice by affecting sugar levels via the TB1–RCN22–RbcL module

As an important yield component, rice tiller number controls panicle number and determines grain yield. Regulation of rice tiller number by chloroplast pentatricopeptide repeat (PPR) proteins has not been reported previously. Here, we report the rice reduced culm number22 (rcn22) mutant, which produces few tillers owing to suppressed tiller bud elongation. Map-based cloning revealed that RCN22 encodes a chloroplast-localized P-type PPR protein. We found that RCN22 specifically binds to the 5′ UTR of RbcL mRNA (encoding the large subunit of Rubisco) and enhances its stability. The reduced abundance of RbcL mRNA in rcn22 leads to a lower photosynthetic rate and decreased sugar levels. Consequently, transcript levels of DWARF3 (D3) and TEOSINTE BRANCHED1 (TB1) (which encode negative regulators of tiller bud elongation) are increased, whereas protein levels of the positive regulator DWARF53 (D53) are decreased. Furthermore, high concentrations of sucrose can rescue the tiller bud growth defect of the rcn22 mutant. On the other hand, TB1 directly binds to the RCN22 promoter and downregulates its expression. The tb1/rcn22 double mutant shows a tillering phenotype similar to that of rcn22. Our results suggest that the TB1–RCN22–RbcL module plays a vital role in rice tiller bud elongation by affecting sugar levels.

The genomic potential of photosynthesis in piconanoplankton is functionally redundant but taxonomically structured at a global scale.

Carbon fixation is a key metabolic function shaping marine life, but the underlying taxonomic and functional diversity involved is only partially understood. Using metagenomic resources targeted at marine piconanoplankton, we provide a reproducible machine learning framework to derive the potential biogeography of genomic functions through the multi-output regression of gene read counts on environmental climatologies. Leveraging the Marine Atlas of Tara Oceans Unigenes, we investigate the genomic potential of primary production in the global ocean. The latter is performed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) and is often associated with carbon concentration mechanisms in piconanoplankton, major marine unicellular photosynthetic organisms. We show that the genomic potential supporting C4 enzymes and RUBISCO exhibits strong functional redundancy and important affinity toward tropical oligotrophic waters. This redundancy is taxonomically structured by the dominance of Mamiellophyceae and Prymnesiophyceae in mid and high latitudes. These findings enhance our understanding of the relationship between functional and taxonomic diversity of microorganisms and environmental drivers of key biogeochemical cycles.

Molecular Identification Validates Morphological Identification of Javanese Cardamom from Banyumas in Central Java, Indonesia

Cardamom is one of the prominent plants with significant economic value in the Banyumas Regency, Central Java, Indonesia. Although Javanese cardamom is traditionally categorized under Amomum compactum, the morphological variations observed create ambiguity about its exact species status. DNA barcoding using the maturase K (matK) and ribulose-bisphosphate carboxylase (rbcL) genes is proven as a reliable technique to elucidate the taxonomic status of morphological variable plant cultivars. This study aimed to characterize cardamom from Banyumas Regency using morphological and molecular approaches for taxonomic status identification and genetic diversity evaluation. The matK and rbcL genes were selected as genetic markers and sequenced using a bidirectional sequencing technique. Morphological examination showed significant color variations at the cardamom stem base. All samples had high genetic identities to reference species in databases and were supported by high query cover and zero e-values. Therefore, molecular characterization, alongside geographic distribution assessment, established that this plant belongs to a single species, Amomum compactum. Additionally, the analysis conducted showed a low level of genetic diversity, as evidenced by haplotype and nucleotide diversity. Low-level genetic diversity provides additional data to convince that cardamon in Banyumas Regency belongs to a single species. These results are essential data in seed selection for further cultivation.

Singlet-Oxygen-Mediated Regulation of Photosynthesis-Specific Genes: A Role for Reactive Electrophiles in Signal Transduction.

During photosynthesis, reactive oxygen species (ROS) are formed, including hydrogen peroxide (H2O2) and singlet oxygen (1O2), which have putative roles in signalling, but their involvement in photosynthetic acclimation is unclear. Due to extreme reactivity and a short lifetime, 1O2 signalling occurs via its reaction products, such as oxidised poly-unsaturated fatty acids in thylakoid membranes. The resulting lipid peroxides decay to various aldehydes and reactive electrophile species (RES). Here, we investigated the role of ROS in the signal transduction of high light (HL), focusing on GreenCut2 genes unique to photosynthetic organisms. Using RNA seq. data, the transcriptional responses of Chlamydomonas reinhardtii to 2 h HL were compared with responses under low light to exogenous RES (acrolein; 4-hydroxynonenal), β-cyclocitral, a β-carotene oxidation product, as well as Rose Bengal, a 1O2-producing photosensitiser, and H2O2. HL induced significant (p < 0.05) up- and down-regulation of 108 and 23 GreenCut2 genes, respectively. Of all HL up-regulated genes, over half were also up-regulated by RES, including RBCS1 (ribulose bisphosphate carboxylase small subunit), NPQ-related PSBS1 and LHCSR1. Furthermore, 96% of the genes down-regulated by HL were also down-regulated by 1O2 or RES, including CAO1 (chlorophyllide-a oxygnease), MDH2 (NADP-malate dehydrogenase) and PGM4 (phosphoglycerate mutase) for glycolysis. In comparison, only 0-4% of HL-affected GreenCut2 genes were similarly affected by H2O2 or β-cyclocitral. Overall, 1O2 plays a significant role in signalling during the initial acclimation of C. reinhardtii to HL by up-regulating photo-protection and carbon assimilation and down-regulating specific primary metabolic pathways. Our data support that this pathway involves RES.