Photosynthesis

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    The central circadian clock proteins CCA1 and LHY regulate iron homeostasis in Arabidopsis
    Gang Xu, Zhimin Jiang, Haiyang Wang and Rongcheng Lin
    J Integr Plant Biol 2019, 61 (2): 168-181.  
    DOI: 10.1111/jipb.12696
    Abstract (Browse 265)  |   Save
    Circadian clock is the endogenous time-keeping machinery that synchronizes an organism's metabolism, behavior, and physiology to the daily light-dark circles, thereby contributing to organismal fitness. Iron (Fe) is an essential micronutrient for all organisms and it plays important roles in diverse processes of plant growth and development. Here, we show that, in Arabidopsis thaliana, loss of the central clock genes, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), results in both reduced Fe uptake and photosynthetic efficiency, whereas CCA1 overexpression confers the opposite effects. We show that root Fe(III) reduction activity, and expression of FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER 1 (IRT1) exhibit circadian oscillations, which are disrupted in the cca1 lhy double mutant. Furthermore, CCA1 directly binds to the specific regulatory regions of multiple Fe homeostasis genes and activates their expression. Thus, this study established that, in plants, CCA1 and LHY function as master regulators that maintain cyclic Fe homeostasis.
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    Arabidopsis DXO1 possesses deNADding and exonuclease activities and its mutation affects defense-related and photosynthetic gene expression
    Shuying Pan, Kai-en Li, Wei Huang, Huan Zhong, Huihui Wu, Yuan Wang, He Zhang, Zongwei Cai, Hongwei Guo, Xuemei Chen and Yiji Xia
    J Integr Plant Biol 2020, 62 (7): 967-983.  
    doi: 10.1111/jipb.12867
    Abstract (Browse 455)  |   Save

    RNA capping and decapping tightly coordinate with transcription, translation, and RNA decay to regulate gene expression. Proteins in the DXO/Rai1 family have been implicated in mRNA decapping and decay, and mammalian DXO was recently found to also function as a decapping enzyme for NAD+‐capped RNAs (NAD‐RNA). The Arabidopsis genome contains a single gene encoding a DXO/Rai1 protein, AtDXO1. Here we show that AtDXO1 possesses both NAD‐RNA decapping activity and 5ʹ‐3ʹ exonuclease activity but does not hydrolyze the m7G cap. The atdxo1 mutation increased the stability of NAD‐RNAs and led to pleiotropic phenotypes, including severe growth retardation, pale color, and multiple developmental defects. Transcriptome profiling analysis showed that the atdxo1 mutation resulted in upregulation of defense‐related genes but downregulation of photosynthesis‐related genes. The autoimmunity phenotype of the mutant could be suppressed by either eds1 or npr1 mutation. However, the various phenotypes associated with the atdxo1 mutant could be complemented by an enzymatically inactive AtDXO1. The atdxo1 mutation apparently enhances post‐transcriptional gene silencing by elevating levels of siRNAs. Our study indicates that AtDXO1 regulates gene expression in various biological and physiological processes through its pleiotropic molecular functions in mediating RNA processing and decay.

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    Plastid ribosomal protein LPE2 is involved in photosynthesis and the response to C/N balance in Arabidopsis thaliana
    Xiaoxiao Dong, Sujuan Duan, Hong-Bin Wang and Hong-Lei Jin
    J Integr Plant Biol 2020, 62 (9): 1418-1432.  
    doi: 10.1111/jipb.12907
    Abstract (Browse 403)  |   Save

    The balance between cellular carbon (C) and nitrogen (N) must be tightly coordinated to sustain optimal growth and development in plants. In chloroplasts, photosynthesis converts inorganic C to organic C, which is important for maintenance of C content in plant cells. However, little is known about the role of chloroplasts in C/N balance. Here, we identified a nuclear‐encoded protein LOW PHOTOSYNTHETIC EFFICIENCY2 (LPE2) that it is required for photosynthesis and C/N balance in Arabidopsis. LPE2 is specifically localized in the chloroplast. Both loss‐of‐function mutants, lpe2‐1 and lpe2‐2, showed lower photosynthetic activity, characterized by slower electron transport and lower PSII quantum yield than the wild type. Notably, LPE2 is predicted to encode the plastid ribosomal protein S21 (RPS21). Deficiency of LPE2 significantly perturbed the thylakoid membrane composition and plastid protein accumulation, although the transcription of plastid genes is not affected obviously. More interestingly, transcriptome analysis indicated that the loss of LPE2 altered the expression of C and N response related genes in nucleus, which is confirmed by quantitative real‐time‐polymerase chain reaction. Moreover, deficiency of LPE2 suppressed the response of C/N balance in physiological level. Taken together, our findings suggest that LPE2 plays dual roles in photosynthesis and the response to C/N balance.

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    Pentatricopeptide repeat protein PHOTOSYSTEM I BIOGENESIS FACTOR2 is required for splicing of ycf3
    Xuemei Wang, Zhipan Yang, Yi Zhang, Wen Zhou, Aihong Zhang and Congming Lu
    J Integr Plant Biol 2020, 62 (11): 1741-1761.  
    DOI: 10.1111/jipb.12936
    Abstract (Browse 326)  |   Save

    To gain a better understanding of the molecular mechanisms of photosystem I (PSI) biogenesis, we characterized the Arabidopsis thaliana photosystem I biogenesis factor 2 (pbf2) mutant, which lacks PSI complex. PBF2 encodes a P‐class pentatricopeptide repeat (PPR) protein. In the pbf2 mutants, we observed a striking decrease in the transcript level of only one gene, the chloroplast gene ycf3, which is essential for PSI assembly. Further analysis of ycf3 transcripts showed that PBF2 is specifically required for the splicing of ycf3 intron 1. Computational prediction of binding sequences and electrophoretic mobility shift assays reveal that PBF2 specifically binds to a sequence in ycf3 intron 1. Moreover, we found that PBF2 interacted with two general factors for group II intron splicing CHLOROPLAST RNA SPLICING2‐ASSOCIATED FACTOR1 (CAF1) and CAF2, and facilitated the association of these two factors with ycf3 intron 1. Our results suggest that PBF2 is specifically required for the splicing of ycf3 intron 1 through cooperating with CAF1 and CAF2. Our results also suggest that additional proteins are required to contribute to the specificity of CAF‐dependent group II intron splicing.

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    Light participates in the auxin‐dependent regulation of plant growth
    Bingsheng Lv, Jiayong Zhu, Xiangpei Kong and Zhaojun Ding
    J Integr Plant Biol 2021, 63 (5): 819-822.  
    doi: 10.1111/jipb.13036
    Abstract (Browse 378)  |   Save
    Light is the energy source for plant photosynthesis and influences plant growth and development. Through multiple photoreceptors, plant interprets light signals through various downstream phytohormones such as auxin. Recently, Chen et al. (2020) uncover a new layer of regulation in IPyA pathway of auxin biosynthesis by light. Here we highlight recent studies about how light controls plant growth through regulating auxin biosynthesis and signaling.
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    From genes to networks: The genetic control of leaf development
    Hongfeng Wang, Fanjiang Kong and Chuanen Zhou
    J Integr Plant Biol 2021, 63 (7): 1181-1196.  
    doi: 10.1111/jipb.13084
    Abstract (Browse 402)  |   Save
    Substantial diversity exists for both the size and shape of the leaf, the main photosynthetic organ of flowering plants. The two major forms of leaf are simple leaves, in which the leaf blade is undivided, and compound leaves, which comprise several leaflets. Leaves form at the shoot apical meristem from a group of undifferentiated cells, which first establish polarity, then grow and differentiate. Each of these processes is controlled by a combination of transcriptional regulators, microRNAs and phytohormones. The present review documents recent advances in our understanding of how these various factors modulate the development of both simple leaves (focusing mainly on the model plant Arabidopsis thaliana) and compound leaves (focusing mainly on the model legume species Medicago truncatula).
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    Structure of plant photosystem I−light harvesting complex I supercomplex at 2.4 Å resolution
    Jie Wang, Long‐Jiang Yu, Wenda Wang, Qiujing Yan, Tingyun Kuang, Xiaochun Qin and Jian‐Ren Shen
    J Integr Plant Biol 2021, 63 (7): 1367-1381.  
    DOI: 10.1111/jipb.13095
    Abstract (Browse 263)  |   Save
    Photosystem I (PSI) is one of the two photosystems in photosynthesis, and performs a series of electron transfer reactions leading to the reduction of ferredoxin. In higher plants, PSI is surrounded by four light-harvesting complex I (LHCI) subunits, which harvest and transfer energy efficiently to the PSI core. The crystal structure of PSI-LHCI supercomplex has been analyzed up to 2.6 Å resolution, providing much information on the arrangement of proteins and cofactors in this complicated supercomplex. Here we have optimized crystallization conditions, and analyzed the crystal structure of PSI-LHCI at 2.4 Å resolution. Our structure showed some shift of the LHCI, especially the Lhca4 subunit, away from the PSI core, suggesting the indirect connection and inefficiency of energy transfer from this Lhca subunit to the PSI core. We identified five new lipids in the structure, most of them are located in the gap region between the Lhca subunits and the PSI core. These lipid molecules may play important roles in binding of the Lhca subunits to the core, as well as in the assembly of the supercomplex. The present results thus provide novel information for the elucidation of the mechanisms for the light-energy harvesting, transfer and assembly of this supercomplex.
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    A unique photosystem I reaction center from a chlorophyll d-containing cyanobacterium Acaryochloris marina
    Caihuang Xu, Qingjun Zhu, Jing‐Hua Chen, Liangliang Shen, Xiaohan Yi, Zihui Huang, Wenda Wang, Min Chen, Tingyun Kuang, Jian‐Ren Shen, Xing Zhang and Guangye Han
    J Integr Plant Biol 2021, 63 (10): 1740-1752.  
    doi: 10.1111/jipb.13113
    Abstract (Browse 223)  |   Save
    Photosystem I (PSI) is a large protein supercomplex that catalyzes the light-dependent oxidation of plastocyanin (or cytochrome c6) and the reduction of ferredoxin. This catalytic reaction is realized by a transmembrane electron transfer chain consisting of primary electron donor (a special chlorophyll (Chl) pair) and electron acceptors A0, A1, and three Fe4S4 clusters, FX, FA, and FB. Here we report the PSI structure from a Chl d-dominated cyanobacterium Acaryochloris marina at 3.3 Å resolution obtained by single-particle cryo-electron microscopy. The A. marina PSI exists as a trimer with three identical monomers. Surprisingly, the structure reveals a unique composition of electron transfer chain in which the primary electron acceptor A0 is composed of two pheophytin a rather than Chl a found in any other well-known PSI structures. A novel subunit Psa27 is observed in the A. marina PSI structure. In addition, 77 Chls, 13 α-carotenes, two phylloquinones, three Fe-S clusters, two phosphatidyl glycerols, and one monogalactosyl-diglyceride were identified in each PSI monomer. Our results provide a structural basis for deciphering the mechanism of photosynthesis in a PSI complex with Chl d as the dominating pigments and absorbing far-red light.
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    The Arabidopsis NuA4 histone acetyltransferase complex is required for chlorophyll biosynthesis and photosynthesis
    Jin‐Xing Zhou, Xiao‐Min Su, Si‐Yao Zheng, Chan‐Juan Wu, Yin‐Na Su, Zhaodi Jiang, Lin Li, She Chen and Xin‐Jian He
    J Integr Plant Biol 2022, 64 (4): 901-914.  
    DOI: 10.1111/jipb.13227
    Abstract (Browse 299)  |   Save

    Although two Enhancer of Polycomb-like proteins, EPL1A and EPL1B (EPL1A/B), are known to be conserved and characteristic subunits of the NuA4-type histone acetyltransferase complex in Arabidopsis thaliana, the biological function of EPL1A/B and the mechanism by which EPL1A/B function in the complex remain unknown. Here, we report that EPL1A/B are required for the histone acetyltransferase activity of the NuA4 complex on the nucleosomal histone H4 in vitro and for the enrichment of histone H4K5 acetylation at thousands of protein-coding genes in vivo. Our results suggest that EPL1A/B are required for linking the NuA4 catalytic subunits HISTONE ACETYLTRANSFERASE OF THE MYST FAMILY 1(HAM1) and HAM2 with accessory subunits in the NuA4 complex. EPL1A/B function redundantly in regulating plant development especially in chlorophyll biosynthesis and de-etiolation. The EPL1A/B-dependent transcription and H4K5Ac are enriched at genes involved in chlorophyll biosynthesis and photosynthesis. We also find that EAF6, another characteristic subunit of the NuA4 complex, contributes to de-etiolation. These results suggest that the Arabidopsis NuA4 complex components function as a whole to mediate histone acetylation and transcriptional activation specifically at light-responsive genes and are critical for photomorphogenesis.

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    Cited: Web of Science(9)
      
    Vitamin B1 THIAMIN REQUIRING1 synthase mediates the maintenance of chloroplast function by regulating sugar and fatty acid metabolism in rice
    Yanshen Nie, Li Yu, Lianlian Mao, Wenxuan Zou, Xiufeng Zhang and Jie Zhao
    J Integr Plant Biol 2022, 64 (8): 1575-1595.  
    DOI: 10.1111/jipb.13283
    Abstract (Browse 362)  |   Save

    Vitamin B1 (VB1), including thiamin, thiamin monophosphate (TMP), and thiamin pyrophosphate (TPP), is an essential micronutrient for all living organisms. Nevertheless, the precise function of VB1 in rice remains unclear. Here, we described a VB1 auxotrophic mutant, chlorotic lethal seedling (cles) from the mutation of OsTH1, which displayed collapsed chloroplast membrane system and decreased pigment content. OsTH1 encoded a phosphomethylpyrimidine kinase/thiamin-phosphate pyrophosphorylase, and was expressed in various tissues, especially in seedlings, leaves, and young panicles. The VB1 content in cles was markedly reduced, despite an increase in the expression of VB1 synthesis genes. The decreased TPP content affected the tricarboxylic acid cycle, pentose phosphate pathway, and de novo fatty acid synthesis, leading to a reduction in fatty acids (C16:0 and C18:0) and sugars (sucrose and glucose) of cles. Additionally, irregular expression of chloroplast membrane synthesis genes led to membrane collapse. We also found that alternative splicing and translation allowed OsTH1 to be localized to both chloroplast and cytosol. Our study revealed that OsTH1 was an essential enzyme in VB1 biosynthesis and played crucial roles in seedling growth and development by participating in fatty acid and sugar metabolism, providing new perspectives on VB1 function in rice.

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    Cited: Web of Science(1)
      
    High non-photochemical quenching of VPZ transgenic potato plants limits CO2 assimilation under high light conditions and reduces tuber yield under fluctuating light
    Günter G. Lehretz, Anja Schneider, Dario Leister and Uwe Sonnewald
    J Integr Plant Biol 2022, 64 (9): 1821-1832.  
    doi: 10.1111/jipb.13320
    Abstract (Browse 185)  |   Save

    Under natural conditions, photosynthesis has to be adjusted to fluctuating light intensities. Leaves exposed to high light dissipate excess light energy in form of heat at photosystem II (PSII) by a process called non-photochemical quenching (NPQ). Upon fast transition from light to shade, plants lose light energy by a relatively slow relaxation from photoprotection. Combined overexpression of violaxanthin de-epoxidase (VDE), PSII subunit S (PsbS) and zeaxanthin epoxidase (ZEP) in tobacco accelerates relaxation from photoprotection, and increases photosynthetic productivity. In Arabidopsis, expression of the same three genes (VPZ) resulted in a more rapid photoprotection but growth of the transgenic plants was impaired. Here we report on VPZ expressing potato plants grown under various light regimes. Similar to tobacco and Arabidopsis, induction and relaxation of NPQ was accelerated under all growth conditions tested, but did not cause an overall increased photosynthetic rate or growth of transgenic plants. Tuber yield of VPZ expressing plants was unaltered as compared to control plants under constant light conditions and even decreased under fluctuating light conditions. Under control conditions, levels of the phytohormone abscisic acid (ABA) were found to be elevated, indicating an increased violaxanthin availability in VPZ plants. However, the increased basal ABA levels did not improve drought tolerance of VPZ transgenic potato plants under greenhouse conditions. The failure to benefit from improved photoprotection is most likely caused by a reduced radiation use efficiency under high light conditions resulting from a too strong NPQ induction. Mitigating this negative effect in the future might help to improve photosynthetic performance in VPZ expressing potato plants.

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    Cited: Web of Science(8)
      
    Quantitative proteomics reveals redox-based functional regulation of photosynthesis under fluctuating light in plants
    Qi Chen, Yixian Xiao, Yu Ming, Rong Peng, Jiliang Hu, Hong‐Bin Wang and Hong‐Lei Jin
    J Integr Plant Biol 2022, 64 (11): 2168-2186.  
    doi: 10.1111/jipb.13348
    Abstract (Browse 382)  |   Save

    Photosynthesis involves a series of redox reactions and is the major source of reactive oxygen species in plant cells. Fluctuating light (FL) levels, which occur commonly in natural environments, affect photosynthesis; however, little is known about the specific effects of FL on the redox regulation of photosynthesis. Here, we performed global quantitative mapping of the Arabidopsis thaliana cysteine thiol redox proteome under constant light and FL conditions. We identified 8857 redox-switched thiols in 4350 proteins, and 1501 proteins that are differentially modified depending on light conditions. Notably, proteins related to photosynthesis, especially photosystem I (PSI), are operational thiol-switching hotspots. Exposure of wild-type A. thaliana to FL resulted in decreased PSI abundance, stability, and activity. Interestingly, in response to PSI photodamage, more of the PSI assembly factor PSA3 dynamically switches to the reduced state. Furthermore, the Cys199 and Cys200 sites in PSA3 are necessary for its full function. Moreover, thioredoxin m (Trx m) proteins play roles in redox switching of PSA3, and are required for PSI activity and photosynthesis. This study thus reveals a mechanism for redox-based regulation of PSI under FL, and provides insight into the dynamic acclimation of photosynthesis in a changing environment.

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    Cited: Web of Science(5)
      
    Cryo-electron microscopy structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium
    Jing-Hua Chen, Weiwei Wang, Chen Wang, Tingyun Kuang, Jian-Ren Shen, Xing Zhang
    J Integr Plant Biol 2023, 65 (1): 223-234.  
    DOI: 10.1111/jipb.13367
    Abstract (Browse 164)  |   Save
    The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna–Matthews–Olson (FMO). Functionally, FMO transfers the absorbed energy from a huge peripheral light-harvesting antenna named chlorosome to the RC core where charge separation occurs. In vivo, one RC was found to bind two FMOs, however, the intact structure of RCC as well as the energy transfer mechanism within RCC remain to be clarified. Here we report a structure of intact RCC which contains a RC core and two FMO trimers from a thermophilic green sulfur bacterium Chlorobaculum tepidum at 2.9?? resolution by cryo-electron microscopy. The second FMO trimer is attached at the cytoplasmic side asymmetrically relative to the first FMO trimer reported previously. We also observed two new subunits (PscE and PscF) and the N-terminal transmembrane domain of a cytochrome-containing subunit (PscC) in the structure. These two novel subunits possibly function to facilitate the binding of FMOs to RC core and to stabilize the whole complex. A new bacteriochlorophyll (numbered as 816) was identified at the interspace between PscF and PscA-1, causing an asymmetrical energy transfer from the two FMO trimers to RC core. Based on the structure, we propose an energy transfer network within this photosynthetic apparatus.
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    Cited: Web of Science(3)
      
    GmFtsH25 overexpression increases soybean seed yield by enhancing photosynthesis and photosynthates
    Li Wang, Yuming Yang, Zhongyi Yang, Wenlong Li, Dezhou Hu, Huilian Yu, Xiao Li, Hao Cheng, Guizhen Kan, Zhijun Che, Dan Zhang, Hengyou Zhang, Hui Wang, Fang Huang and Deyue Yu
    J Integr Plant Biol 2023, 65 (4): 1026-1040.  
    DOI: 10.1111/jipb.13405
    Abstract (Browse 591)  |   Save
    Increasing plant photosynthetic capacity is a promising approach to boost yields, but it is particularly challenging in C3 crops, such as soybean (Glycine max (L.) Merr.). Here, we identified GmFtsH25, encoding a member of the filamentation temperature‐sensitive protein H protease family, as a major gene involved in soybean photosynthesis, using linkage mapping and a genome‐wide association study. Overexpressing GmFtsH25 resulted in more grana thylakoid stacks in chloroplasts and increased photosynthetic efficiency and starch content, while knocking out GmFtsH25 produced the opposite phenotypes. GmFtsH25 interacted with photosystem I light harvesting complex 2 (GmLHCa2), and this interaction may contribute to the observed enhanced photosynthesis. GmFtsH25 overexpression lines had superior yield traits, such as yield per plant, compared to the wild type and knockout lines. Additionally, we identified an elite haplotype of GmFtsH25, generated by natural mutations, which appears to have been selected during soybean domestication. Our study sheds light on the molecular mechanism by which GmFtsH25 modulates photosynthesis and provides a promising strategy for improving the yields of soybean and other crops.
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    Cited: Web of Science(4)
      
    Carotenoid isomerase regulates rice tillering and grain productivity by its biosynthesis pathway
    Chaoqing Ding, Zhengji Shao, Yuping Yan, Guangheng Zhang, Dali Zeng, Li Zhu, Jiang Hu, Zhenyu Gao, Guojun Dong, Qian Qian and Deyong Ren
    J Integr Plant Biol 2024, 66 (2): 172-175.  
    doi: 10.1111/jipb.13617
    Abstract (Browse 183)  |   Save
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    Structural insights into the unusual core photocomplex from a triply extremophilic purple bacterium, Halorhodospira halochloris
    Chen-Hui Qi, Guang-Lei Wang, Fang-Fang Wang, Jie Wang, Xiang-Ping Wang, Mei-Juan Zou, Fei Ma, Michael T. Madigan, Yukihiro Kimura, Zheng-Yu Wang-Otomo, Long-Jiang Yu
    J Integr Plant Biol 2024, 66 (10): 2262-2272.  
    doi: 10.1111/jipb.13628
    Abstract (Browse 82)  |   Save
    Halorhodospira (Hlr.) halochloris is a triply extremophilic phototrophic purple sulfur bacterium, as it is thermophilic, alkaliphilic, and extremely halophilic. The light-harvesting-reaction center (LH1-RC) core complex of this bacterium displays an LH1-Qy transition at 1,016 nm, which is the lowest-energy wavelength absorption among all known phototrophs. Here we report the cryo-EM structure of the LH1-RC at 2.42 Å resolution. The LH1 complex forms a tricyclic ring structure composed of 16 αβγ-polypeptides and one αβ-heterodimer around the RC. From the cryo-EM density map, two previously unrecognized integral membrane proteins, referred to as protein G and protein Q, were identified. Both of these proteins are single transmembrane-spanning helices located between the LH1 ring and the RC L- subunit and are absent from the LH1-RC complexes of all other purple bacteria of which the structures have been determined so far. Besides bacteriochlorophyll b molecules (B1020) located on the periplasmic side of the Hlr. halochloris membrane, there are also two arrays of bacteriochlorophyll b molecules (B800 and B820) located on the cytoplasmic side. Only a single copy of a carotenoid (lycopene) was resolved in the Hlr. halochloris LH1-α3β3 and this was positioned within the complex. The potential quinone channel should be the space between the LH1-α3β3 that accommodates the single lycopene but does not contain a γ-polypeptide, B800 and B820. Our results provide a structural explanation for the unusual Qy red shift and carotenoid absorption in the Hlr. halochloris spectrum and reveal new insights into photosynthetic mechanisms employed by a species that thrives under the harshest conditions of any phototrophic microorganism known.
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    The genome of Eleocharis vivipara elucidates the genetics of C3–C4 photosynthetic plasticity and karyotype evolution in the Cyperaceae
    Hongbing Liu, Hang Zhao, Yanwen Zhang, Xiuli Li, Yi Zuo, Zhen Wu, Kaining Jin, Wenfei Xian, Wenzheng Wang, Weidong Ning, Zijian Liu, Xiaoxiao Zhao, Lei Wang, Rowan F. Sage, Tiegang Lu, Matt Stata, Shifeng Cheng
    J Integr Plant Biol 2024, 66 (11): 2505-2527.  
    doi: 10.1111/jipb.13765
    Abstract (Browse 68)  |   Save
    Eleocharis vivipara, an amphibious sedge in the Cyperaceae family, has several remarkable properties, most notably its alternate use of C3 photosynthesis underwater and C4 photosynthesis on land. However, the absence of genomic data has hindered its utility for evolutionary and genetic research. Here, we present a high-quality genome for E. vivipara, representing the first chromosome-level genome for the Eleocharis genus, with an approximate size of 965.22 Mb mainly distributed across 10 chromosomes. Its Hi–C pattern, chromosome clustering results, and one-to-one genome synteny across two subgroups indicates a tetraploid structure with chromosome count 2n = 4x = 20. Phylogenetic analysis suggests that E. vivipara diverged from Cyperus esculentus approximately 32.96 million years ago (Mya), and underwent a whole-genome duplication (WGD) about 3.5 Mya. Numerous fusion and fission events were identified between the chromosomes of E. vivipara and its close relatives. We demonstrate that E. vivipara has holocentromeres, a chromosomal feature which can maintain the stability of such chromosomal rearrangements. Experimental transplantation and cross-section studies showed its terrestrial culms developed C4 Kranz anatomy with increased number of chloroplasts in the bundle sheath (BS) cells. Gene expression and weighted gene co-expression network analysis (WGCNA) showed overall elevated expression of core genes associated with the C4 pathway, and significant enrichment of genes related to modified culm anatomy and photosynthesis efficiency. We found evidence of mixed nicotinamide adenine dinucleotide - malic enzyme and phosphoenolpyruvate carboxykinase type C4 photosynthesis in E. vivipara, and hypothesize that the evolution of C4 photosynthesis predates the WGD event. The mixed type is dominated by subgenome A and supplemented by subgenome B. Collectively, our findings not only shed light on the evolution of E. vivipara and karyotype within the Cyperaceae family, but also provide valuable insights into the transition between C3 and C4 photosynthesis, offering promising avenues for crop improvement and breeding.
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