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Meng F, Ma M, Li S, Liang P, Liang Y, Shi H, Huang S, Su H, Deng Y, Akram MA, Shen X, Feng R, Zhan X, Ma F. Genome-wide identification of light-harvesting chlorophyll a/b-binding (LHC) gene family in tomato and functional analysis of SlLhcb1.11 and SlELIP1 under cold stress. Genomics 2025; 117:111022. [PMID: 40021098 DOI: 10.1016/j.ygeno.2025.111022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 02/19/2025] [Accepted: 02/24/2025] [Indexed: 03/03/2025]
Abstract
Light-harvesting chlorophyll a/b-binding (LHC) proteins, as the antenna complex, collect and transfer light energy to the reaction centers of PSII. They are crucial for abiotic stress responses, especially in the photoprotection under cold stress. However, members of the LHC gene family in tomato (Solanum lycopersicum L.) have not yet been identified. In this study, a total of 39 SlLHC proteins containing the chlorophyll a/b binding domain or light-harvesting-like domain were identified, and classified into four subfamilies: Lhc, Lil, PsbS, and FCII. Further qRT-PCR analysis showed SlLhcb1.11 was inhibited and SlELIP1 was induced at low temperature (4 °C). Subsequently, the result of VIGS experiment showed that silencing SlLhcb1.11 or SlELIP1 genes resulted in lighter leaf color, reduced chlorophyll content, compromised photosynthesis, and decreased cold tolerance in tomato plants. These findings offer novel insights into the structure and function of SlLHC genes, thereby contributing to genetic resources for the development of cold-tolerant tomato germplasm.
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Affiliation(s)
- Fanyi Meng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Mengqiu Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Shanshan Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Pan Liang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Yunfei Liang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Hongyan Shi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Shudi Huang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Huai Su
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Yilin Deng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Muhammad Asif Akram
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Xiaoxia Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Ru Feng
- Ulanqab Agricultural Technology and Popularization Center, Ulanqab, Inner Mongolia Autonomous Region 012000, China
| | - Xiangqiang Zhan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China.
| | - Fang Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China.
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Bassi R, Dall'Osto L. Dissipation of Light Energy Absorbed in Excess: The Molecular Mechanisms. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:47-76. [PMID: 34143647 DOI: 10.1146/annurev-arplant-071720-015522] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Light is essential for photosynthesis. Nevertheless, its intensity widely changes depending on time of day, weather, season, and localization of individual leaves within canopies. This variability means that light collected by the light-harvesting system is often in excess with respect to photon fluence or spectral quality in the context of the capacity of photosynthetic metabolism to use ATP and reductants produced from the light reactions. Absorption of excess light can lead to increased production of excited, highly reactive intermediates, which expose photosynthetic organisms to serious risks of oxidative damage. Prevention and management of such stress are performed by photoprotective mechanisms, which operate by cutting down light absorption, limiting the generation of redox-active molecules, or scavenging reactive oxygen species that are released despite the operation of preventive mechanisms. Here, we describe the major physiological and molecular mechanisms of photoprotection involved in the harmless removal of the excess light energy absorbed by green algae and land plants. In vivo analyses of mutants targeting photosynthetic components and the enhanced resolution of spectroscopic techniques have highlighted specific mechanisms protecting the photosynthetic apparatus from overexcitation. Recent findings unveil a network of multiple interacting elements, the reaction times of which vary from a millisecond to weeks, that continuously maintain photosynthetic organisms within the narrow safety range between efficient light harvesting and photoprotection.
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Affiliation(s)
- Roberto Bassi
- Department of Biotechnology, University of Verona, 37134 Verona, Italy;
| | - Luca Dall'Osto
- Department of Biotechnology, University of Verona, 37134 Verona, Italy;
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LHC-like proteins involved in stress responses and biogenesis/repair of the photosynthetic apparatus. Biochem J 2019; 476:581-593. [PMID: 30765616 DOI: 10.1042/bcj20180718] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/18/2019] [Accepted: 01/21/2019] [Indexed: 01/04/2023]
Abstract
LHC (light-harvesting complex) proteins of plants and algae are known to be involved both in collecting light energy for driving the primary photochemical reactions of photosynthesis and in photoprotection when the absorbed light energy exceeds the capacity of the photosynthetic apparatus. These proteins usually contain three transmembrane (TM) helices which span the thylakoid membranes and bind several chlorophyll, carotenoid and lipid molecules. In addition, the LHC protein family includes LHC-like proteins containing one, two, three or even four TM domains. One-helix proteins are not only present in eukaryotic photosynthetic organisms but also in cyanobacteria where they have been named high light-inducible proteins. These small proteins are probably the ancestors of the members of the extant LHC protein family which arouse through gene duplications, deletions and fusions. During evolution, some of these proteins have diverged and acquired novel functions. In most cases, LHC-like proteins are induced in response to various stress conditions including high light, high salinity, elevated temperature and nutrient limitation. Many of these proteins play key roles in photoprotection, notably in non-photochemical quenching of absorbed light energy. Moreover, some of these proteins appear to be involved in the regulation of chlorophyll synthesis and in the assembly and repair of Photosystem II and also of Photosystem I possibly by mediating the insertion of newly synthesized pigments into the photosynthetic reaction centers.
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Komenda J, Sobotka R. Cyanobacterial high-light-inducible proteins — Protectors of chlorophyll–protein synthesis and assembly. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:288-95. [DOI: 10.1016/j.bbabio.2015.08.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/28/2015] [Accepted: 08/30/2015] [Indexed: 12/24/2022]
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Wang P, Grimm B. Organization of chlorophyll biosynthesis and insertion of chlorophyll into the chlorophyll-binding proteins in chloroplasts. PHOTOSYNTHESIS RESEARCH 2015; 126:189-202. [PMID: 25957270 DOI: 10.1007/s11120-015-0154-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/30/2015] [Indexed: 05/23/2023]
Abstract
Oxygenic photosynthesis requires chlorophyll (Chl) for the absorption of light energy, and charge separation in the reaction center of photosystem I and II, to feed electrons into the photosynthetic electron transfer chain. Chl is bound to different Chl-binding proteins assembled in the core complexes of the two photosystems and their peripheral light-harvesting antenna complexes. The structure of the photosynthetic protein complexes has been elucidated, but mechanisms of their biogenesis are in most instances unknown. These processes involve not only the assembly of interacting proteins, but also the functional integration of pigments and other cofactors. As a precondition for the association of Chl with the Chl-binding proteins in both photosystems, the synthesis of the apoproteins is synchronized with Chl biosynthesis. This review aims to summarize the present knowledge on the posttranslational organization of Chl biosynthesis and current attempts to envision the proceedings of the successive synthesis and integration of Chl into Chl-binding proteins in the thylakoid membrane. Potential auxiliary factors, contributing to the control and organization of Chl biosynthesis and the association of Chl with the Chl-binding proteins during their integration into photosynthetic complexes, are discussed in this review.
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Affiliation(s)
- Peng Wang
- Institute of Biology/Plant Physiology, Humboldt-University Berlin, Philippstraße 13, 10115, Berlin, Germany
| | - Bernhard Grimm
- Institute of Biology/Plant Physiology, Humboldt-University Berlin, Philippstraße 13, 10115, Berlin, Germany.
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Regulation of the scp Genes in the Cyanobacterium Synechocystis sp. PCC 6803--What is New? Molecules 2015; 20:14621-37. [PMID: 26274949 PMCID: PMC6331805 DOI: 10.3390/molecules200814621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 08/05/2015] [Accepted: 08/07/2015] [Indexed: 11/18/2022] Open
Abstract
In the cyanobacterium Synechocystis sp. PCC 6803 there are five genes encoding small CAB-like (SCP) proteins, which have been shown to be up-regulated under stress. Analyses of the promoter sequences of the scp genes revealed the existence of an NtcA binding motif in two scp genes, scpB and scpE. Binding of NtcA, the key transcriptional regulator during nitrogen stress, to the promoter regions was shown by electrophoretic mobility shift assay. The metabolite 2-oxoglutarate did not increase the affinity of NtcA for binding to the promoters of scpB and scpE. A second motif, the HIP1 palindrome 5ʹ GGCGATCGCC 3ʹ, was detected in the upstream regions of scpB and scpC. The transcription factor encoded by sll1130 has been suggested to recognize this motif to regulate heat-responsive genes. Our data suggest that HIP1 is not a regulatory element within the scp genes. Further, the presence of the high light regulatory (HLR1) motif was confirmed in scpB-E, in accordance to their induced transcriptions in cells exposed to high light. The HLR1 motif was newly discovered in eight additional genes.
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Knoppová J, Sobotka R, Tichý M, Yu J, Konik P, Halada P, Nixon PJ, Komenda J. Discovery of a chlorophyll binding protein complex involved in the early steps of photosystem II assembly in Synechocystis. THE PLANT CELL 2014; 26:1200-12. [PMID: 24681620 PMCID: PMC4001378 DOI: 10.1105/tpc.114.123919] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Efficient assembly and repair of the oxygen-evolving photosystem II (PSII) complex is vital for maintaining photosynthetic activity in plants, algae, and cyanobacteria. How chlorophyll is delivered to PSII during assembly and how vulnerable assembly complexes are protected from photodamage are unknown. Here, we identify a chlorophyll and β-carotene binding protein complex in the cyanobacterium Synechocystis PCC 6803 important for formation of the D1/D2 reaction center assembly complex. It is composed of putative short-chain dehydrogenase/reductase Ycf39, encoded by the slr0399 gene, and two members of the high-light-inducible protein (Hlip) family, HliC and HliD, which are small membrane proteins related to the light-harvesting chlorophyll binding complexes found in plants. Perturbed chlorophyll recycling in a Ycf39-null mutant and copurification of chlorophyll synthase and unassembled D1 with the Ycf39-Hlip complex indicate a role in the delivery of chlorophyll to newly synthesized D1. Sequence similarities suggest the presence of a related complex in chloroplasts.
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Affiliation(s)
- Jana Knoppová
- Institute of Microbiology, Academy of Sciences, 37981 Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Roman Sobotka
- Institute of Microbiology, Academy of Sciences, 37981 Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Martin Tichý
- Institute of Microbiology, Academy of Sciences, 37981 Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Jianfeng Yu
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, London SW7 2AZ, United Kingdom
| | - Peter Konik
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Petr Halada
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences, 14220 Praha 4-Krč, Czech Republic
| | - Peter J. Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, London SW7 2AZ, United Kingdom
| | - Josef Komenda
- Institute of Microbiology, Academy of Sciences, 37981 Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
- Address correspondence to
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Takahashi K, Takabayashi A, Tanaka A, Tanaka R. Functional analysis of light-harvesting-like protein 3 (LIL3) and its light-harvesting chlorophyll-binding motif in Arabidopsis. J Biol Chem 2013; 289:987-99. [PMID: 24275650 DOI: 10.1074/jbc.m113.525428] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The light-harvesting complex (LHC) constitutes the major light-harvesting antenna of photosynthetic eukaryotes. LHC contains a characteristic sequence motif, termed LHC motif, consisting of 25-30 mostly hydrophobic amino acids. This motif is shared by a number of transmembrane proteins from oxygenic photoautotrophs that are termed light-harvesting-like (LIL) proteins. To gain insights into the functions of LIL proteins and their LHC motifs, we functionally characterized a plant LIL protein, LIL3. This protein has been shown previously to stabilize geranylgeranyl reductase (GGR), a key enzyme in phytol biosynthesis. It is hypothesized that LIL3 functions to anchor GGR to membranes. First, we conjugated the transmembrane domain of LIL3 or that of ascorbate peroxidase to GGR and expressed these chimeric proteins in an Arabidopsis mutant lacking LIL3 protein. As a result, the transgenic plants restored phytol-synthesizing activity. These results indicate that GGR is active as long as it is anchored to membranes, even in the absence of LIL3. Subsequently, we addressed the question why the LHC motif is conserved in the LIL3 sequences. We modified the transmembrane domain of LIL3, which contains the LHC motif, by substituting its conserved amino acids (Glu-171, Asn-174, and Asp-189) with alanine. As a result, the Arabidopsis transgenic plants partly recovered the phytol-biosynthesizing activity. However, in these transgenic plants, the LIL3-GGR complexes were partially dissociated. Collectively, these results indicate that the LHC motif of LIL3 is involved in the complex formation of LIL3 and GGR, which might contribute to the GGR reaction.
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Affiliation(s)
- Kaori Takahashi
- From the Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan and
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Kelly L, Ding H, Huang KH, Osburne MS, Chisholm SW. Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent. ISME JOURNAL 2013; 7:1827-41. [PMID: 23657361 DOI: 10.1038/ismej.2013.58] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 02/22/2013] [Accepted: 03/04/2013] [Indexed: 11/09/2022]
Abstract
Viruses that infect marine cyanobacteria-cyanophages-often carry genes with orthologs in their cyanobacterial hosts, and the frequency of these genes can vary with habitat. To explore habitat-influenced genomic diversity more deeply, we used the genomes of 28 cultured cyanomyoviruses as references to identify phage genes in three ocean habitats. Only about 6-11% of genes were consistently observed in the wild, revealing high gene-content variability in these populations. Numerous shared phage/host genes differed in relative frequency between environments, including genes related to phosphorous acquisition, photorespiration, photosynthesis and the pentose phosphate pathway, possibly reflecting environmental selection for these genes in cyanomyovirus genomes. The strongest emergent signal was related to phosphorous availability; a higher fraction of genomes from relatively low-phosphorus environments-the Sargasso and Mediterranean Sea-contained host-like phosphorus assimilation genes compared with those from the N. Pacific Gyre. These genes are known to be upregulated when the host is phosphorous starved, a response mediated by pho box motifs in phage genomes that bind a host regulatory protein. Eleven cyanomyoviruses have predicted pho boxes upstream of the phosphate-acquisition genes pstS and phoA; eight of these have a conserved cyanophage-specific gene (PhCOG173) between the pho box and pstS. PhCOG173 is also found upstream of other shared phage/host genes, suggesting a unique regulatory role. Pho boxes are found upstream of high light-inducible (hli) genes in cyanomyoviruses, suggesting that this motif may have a broader role than regulating phosphorous-stress responses in infected hosts or that these hlis are involved in the phosphorous-stress response.
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Affiliation(s)
- Libusha Kelly
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Storm P, Tibiletti T, Hall M, Funk C. Refolding and enzyme kinetic studies on the ferrochelatase of the cyanobacterium Synechocystis sp. PCC 6803. PLoS One 2013; 8:e55569. [PMID: 23390541 PMCID: PMC3563542 DOI: 10.1371/journal.pone.0055569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/27/2012] [Indexed: 11/19/2022] Open
Abstract
Heme is a cofactor for proteins participating in many important cellular processes, including respiration, oxygen metabolism and oxygen binding. The key enzyme in the heme biosynthesis pathway is ferrochelatase (protohaem ferrolyase, EC 4.99.1.1), which catalyzes the insertion of ferrous iron into protoporphyrin IX. In higher plants, the ferrochelatase enzyme is localized not only in mitochondria, but also in chloroplasts. The plastidic type II ferrochelatase contains a C-terminal chlorophyll a/b (CAB) motif, a conserved hydrophobic stretch homologous to the CAB domain of plant light harvesting proteins and light-harvesting like proteins. This type II ferrochelatase, found in all photosynthetic organisms, is presumed to have evolved from the cyanobacterial ferrochelatase. Here we describe a detailed enzymological study on recombinant, refolded and functionally active type II ferrochelatase (FeCh) from the cyanobacterium Synechocystis sp. PCC 6803. A protocol was developed for the functional refolding and purification of the recombinant enzyme from inclusion bodies, without truncation products or soluble aggregates. The refolded FeCh is active in its monomeric form, however, addition of an N-terminal His6-tag has significant effects on its enzyme kinetics. Strikingly, removal of the C-terminal CAB-domain led to a greatly increased turnover number, kcat, compared to the full length protein. While pigments isolated from photosynthetic membranes decrease the activity of FeCh, direct pigment binding to the CAB domain of FeCh was not evident.
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Affiliation(s)
- Patrik Storm
- Deptartment of Chemistry and Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Tania Tibiletti
- Deptartment of Chemistry and Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Michael Hall
- Deptartment of Chemistry and Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Christiane Funk
- Deptartment of Chemistry and Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- * E-mail:
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Nickelsen J, Rengstl B. Photosystem II assembly: from cyanobacteria to plants. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:609-35. [PMID: 23451783 DOI: 10.1146/annurev-arplant-050312-120124] [Citation(s) in RCA: 238] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Photosystem II (PSII) is an integral-membrane, multisubunit complex that initiates electron flow in oxygenic photosynthesis. The biogenesis of this complex machine involves the concerted assembly of at least 20 different polypeptides as well as the incorporation of a variety of inorganic and organic cofactors. Many factors have recently been identified that constitute an integrative network mediating the stepwise assembly of PSII components. One recurring theme is the subcellular organization of the assembly process in specialized membranes that form distinct biogenesis centers. Here, we review our current knowledge of the molecular components and events involved in PSII assembly and their high degree of evolutionary conservation.
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Affiliation(s)
- Jörg Nickelsen
- Molekulare Pflanzenwissenschaften, Biozentrum Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
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Cheregi O, Vermaas W, Funk C. The search for new chlorophyll-binding proteins in the cyanobacterium Synechocystis sp. PCC 6803. J Biotechnol 2012; 162:124-33. [PMID: 22759916 DOI: 10.1016/j.jbiotec.2012.06.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 06/21/2012] [Accepted: 06/25/2012] [Indexed: 01/24/2023]
Abstract
Light harvesting provides a major challenge in the production of biofuels from microorganisms; while sunlight provides the energy necessary for biomass/biofuel production, at the same time it damages the cells. The genome of Synechocystis sp. PCC 6803 was searched for open reading frames that might code for yet unidentified chlorophyll-binding proteins with low molecular mass that could be involved in stress-adaptation. Amongst 9167 hypothetical ORFs corresponding to potential polypeptides of 100 amino acids or less, two were identified that had the potential to be pigment-binding, because they (i) encoded a potential transmembrane region, (ii) showed sequence similarity with known chlorophyll-binding domains, (iii) were conserved in other cyanobacterial species, and (iv) their codon adaptation index indicated significant translation probability. The two ORFs were located complementary (antisense) and internal to the ferrochelatase (hemH) and the pyruvate dehydrogenase (pdh) genes and therefore were named a-fch and a-pdh, respectively. Transcription of both genes was confirmed; however, no translated proteins could be detected immunologically. Whereas mutations within a-pdh or a-fch did not lead to any obvious phenotype, it is clear that transcripts and proteins over and above the currently known set may play a role in defining the physiology of cyanobacteria and other organisms.
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Affiliation(s)
- Otilia Cheregi
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden.
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Ludwig M, Bryant DA. Synechococcus sp. Strain PCC 7002 Transcriptome: Acclimation to Temperature, Salinity, Oxidative Stress, and Mixotrophic Growth Conditions. Front Microbiol 2012; 3:354. [PMID: 23087677 PMCID: PMC3468840 DOI: 10.3389/fmicb.2012.00354] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 09/15/2012] [Indexed: 12/29/2022] Open
Abstract
Synechococcus sp. strain PCC 7002 is a unicellular, euryhaline cyanobacterium. It is a model organism for studies of cyanobacterial metabolism and has great potential for biotechnological applications. It exhibits an exceptional tolerance of high-light irradiation and shows very rapid growth. The habitats from which this and closely related strains were isolated are subject to changes in several environmental factors, including light, nutrient supply, temperature, and salinity. In this study global transcriptome profiling via RNAseq has been used to perform a comparative and integrated study of global changes in cells grown at different temperatures, at different salinities, and under mixotrophic conditions, when a metabolizable organic carbon source was present. Furthermore, the transcriptomes were investigated for cells that were subjected to a heat shock and that were exposed to oxidative stress. Lower growth temperatures caused relatively minor changes of the transcriptome; the most prominent changes affected fatty acid desaturases. A heat shock caused severe changes of the transcriptome pattern; transcripts for genes associated with major metabolic pathways declined and those for different chaperones increased dramatically. Oxidative stress, however, left the transcript pattern almost unaffected. When grown at high salinity, Synechococcus sp. PCC 7002 had increased expression of genes involved in compatible solute biosynthesis and showed increased mRNA levels for several genes involved in electron transport. Transcripts of two adjacent genes dramatically increased upon growth at high salinity; the respective proteins are putatively involved in coping with oxidative stress and in triggering ion channels. Only minor changes were observed when cells were grown at low salinity or when the growth medium was supplemented with glycerol. However, the transcriptome data suggest that cells must acclimate to excess reducing equivalents when a reduced C-source is present.
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Affiliation(s)
- Marcus Ludwig
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA
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Sinha RK, Komenda J, Knoppová J, Sedlářová M, Pospíšil P. Small CAB-like proteins prevent formation of singlet oxygen in the damaged photosystem II complex of the cyanobacterium Synechocystis sp. PCC 6803. PLANT, CELL & ENVIRONMENT 2012; 35:806-18. [PMID: 22070528 DOI: 10.1111/j.1365-3040.2011.02454.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The cyanobacterial small CAB-like proteins (SCPs) are single-helix membrane proteins mostly associated with the photosystem II (PSII) complex that accumulate under stress conditions. Their function is still ambiguous although they are assumed to regulate chlorophyll (Chl) biosynthesis and/or to protect PSII against oxidative damage. In this study, the effect of SCPs on the PSII-specific light-induced damage and generation of singlet oxygen ((1)O(2)) was assessed in the strains of the cyanobacterium Synechocystis sp. PCC 6803 lacking PSI (PSI-less strain) or lacking PSI together with all SCPs (PSI-less/scpABCDE(-) strain). The light-induced oxidative modifications of the PSII D1 protein reflected by a mobility shift of the D1 protein and by generation of a D1-cytochrome b-559 adduct were more pronounced in the PSI-less/scpABCDE(-) strain. This increased protein oxidation correlated with a faster formation of (1)O(2) as detected by the green fluorescence of Singlet Oxygen Sensor Green assessed by a laser confocal scanning microscopy and by electron paramagnetic resonance spin-trapping technique using 2, 2, 6, 6-tetramethyl-4-piperidone (TEMPD) as a spin trap. In contrast, the formation of hydroxyl radicals was similar in both strains. Our results show that SCPs prevent (1)O(2) formation during PSII damage, most probably by the binding of free Chl released from the damaged PSII complexes.
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Affiliation(s)
- Rakesh Kumar Sinha
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
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Light Stress Proteins in Viruses, Cyanobacteria and Photosynthetic Eukaryota. PHOTOSYNTHESIS 2012. [DOI: 10.1007/978-94-007-1579-0_14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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16
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The Extended Light-Harvesting Complex (LHC) Protein Superfamily: Classification and Evolutionary Dynamics. FUNCTIONAL GENOMICS AND EVOLUTION OF PHOTOSYNTHETIC SYSTEMS 2012. [DOI: 10.1007/978-94-007-1533-2_11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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17
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Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG, Ravel J, Schmidt EW. Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proc Natl Acad Sci U S A 2011; 108:E1423-32. [PMID: 22123943 PMCID: PMC3251135 DOI: 10.1073/pnas.1111712108] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The relationship between tunicates and the uncultivated cyanobacterium Prochloron didemni has long provided a model symbiosis. P. didemni is required for survival of animals such as Lissoclinum patella and also makes secondary metabolites of pharmaceutical interest. Here, we present the metagenomes, chemistry, and microbiomes of four related L. patella tunicate samples from a wide geographical range of the tropical Pacific. The remarkably similar P. didemni genomes are the most complex so far assembled from uncultivated organisms. Although P. didemni has not been stably cultivated and comprises a single strain in each sample, a complete set of metabolic genes indicates that the bacteria are likely capable of reproducing outside the host. The sequences reveal notable peculiarities of the photosynthetic apparatus and explain the basis of nutrient exchange underlying the symbiosis. P. didemni likely profoundly influences the lipid composition of the animals by synthesizing sterols and an unusual lipid with biofuel potential. In addition, L. patella also harbors a great variety of other bacterial groups that contribute nutritional and secondary metabolic products to the symbiosis. These bacteria possess an enormous genetic potential to synthesize new secondary metabolites. For example, an antitumor candidate molecule, patellazole, is not encoded in the genome of Prochloron and was linked to other bacteria from the microbiome. This study unveils the complex L. patella microbiome and its impact on primary and secondary metabolism, revealing a remarkable versatility in creating and exchanging small molecules.
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Affiliation(s)
- Mohamed S. Donia
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112
| | - W. Florian Fricke
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Frédéric Partensky
- Station Biologique de Roscoff, Université Pierre et Marie Curie–Université Paris 6, 29680 Roscoff, France
- Oceanic Plankton Group, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7144, 29680 Roscoff, France
| | - James Cox
- Metabolomics Core Research Facility, University of Utah, Salt Lake City, UT 84112
| | - Sherif I. Elshahawi
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health and Science University, Beaverton, OR 97006
| | - James R. White
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Adam M. Phillippy
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Michael C. Schatz
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Joern Piel
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany; and
| | - Margo G. Haygood
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health and Science University, Beaverton, OR 97006
| | - Jacques Ravel
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112
- Department of Biology, University of Utah, Salt Lake City, UT 84112
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18
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Yao DCI, Brune DC, Vavilin D, Vermaas WFJ. Photosystem II component lifetimes in the cyanobacterium Synechocystis sp. strain PCC 6803: small Cab-like proteins stabilize biosynthesis intermediates and affect early steps in chlorophyll synthesis. J Biol Chem 2011; 287:682-692. [PMID: 22090028 DOI: 10.1074/jbc.m111.320994] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To gain insight in the lifetimes of photosystem II (PSII) chlorophyll and proteins, a combined stable isotope labeling (15N)/mass spectrometry method was used to follow both old and new pigments and proteins. Photosystem I-less Synechocystis cells were grown to exponential or post-exponential phase and then diluted in BG-11 medium with [15N]ammonium and [15N]nitrate. PSII was isolated, and the masses of PSII protein fragments and chlorophyll were determined. Lifetimes of PSII components ranged from 1.5 to 40 h, implying that at least some of the proteins and chlorophyll turned over independently from each other. Also, a significant amount of nascent PSII components accumulated in thylakoids when cells were in post-exponential growth phase. In a mutant lacking small Cab-like proteins (SCPs), most PSII protein lifetimes were unaffected, but the lifetime of chlorophyll and the amount of nascent PSII components that accumulated were decreased. In the absence of SCPs, one of the PSII biosynthesis intermediates, the monomeric PSII complex without CP43, was missing. Therefore, SCPs may stabilize nascent PSII protein complexes. Moreover, upon SCP deletion, the rate of chlorophyll synthesis and the accumulation of early tetrapyrrole precursors were drastically reduced. When [14N]aminolevulinic acid (ALA) was supplemented to 15N-BG-11 cultures, the mutant lacking SCPs incorporated much more exogenous ALA into chlorophyll than the control demonstrating that ALA biosynthesis was impaired in the absence of SCPs. This illustrates the major effects that nonstoichiometric PSII components such as SCPs have on intermediates and assembly but not on the lifetime of PSII proteins.
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Affiliation(s)
- Danny C I Yao
- School of Life Sciences and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287-4501
| | - Daniel C Brune
- School of Life Sciences and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287-4501
| | - Dmitri Vavilin
- School of Life Sciences and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287-4501
| | - Wim F J Vermaas
- School of Life Sciences and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona 85287-4501.
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19
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Shi LX, Hall M, Funk C, Schröder WP. Photosystem II, a growing complex: updates on newly discovered components and low molecular mass proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:13-25. [PMID: 21907181 DOI: 10.1016/j.bbabio.2011.08.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/19/2011] [Accepted: 08/23/2011] [Indexed: 12/12/2022]
Abstract
Photosystem II is a unique complex capable of absorbing light and splitting water. The complex has been thoroughly studied and to date there are more than 40 proteins identified, which bind to the complex either stably or transiently. Another special feature of this complex is the unusually high content of low molecular mass proteins that represent more than half of the proteins. In this review we summarize the recent findings on the low molecular mass proteins (<15kDa) and present an overview of the newly identified components as well. We have also performed co-expression analysis of the genes encoding PSII proteins to see if the low molecular mass proteins form a specific sub-group within the Photosystem II complex. Interestingly we found that the chloroplast-localized genes encoding PSII proteins display a different response to environmental and stress conditions compared to the nuclear localized genes. This article is part of a Special Issue entitled: Photosystem II.
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Affiliation(s)
- Lan-Xin Shi
- Department of Plant Biology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
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20
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The small CAB-like proteins of the cyanobacterium Synechocystis sp. PCC 6803: their involvement in chlorophyll biogenesis for Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1143-51. [PMID: 21605542 DOI: 10.1016/j.bbabio.2011.05.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 05/05/2011] [Accepted: 05/06/2011] [Indexed: 11/23/2022]
Abstract
The five small CAB-like proteins (ScpA-E) of the cyanobacterium Synechocystis sp. PCC 6803 belong to the family of stress-induced light-harvesting-like proteins, but are constitutively expressed in a mutant deficient of Photosystem I (PSI). Using absorption, fluorescence and thermoluminescence measurements this PSI-less strain was compared with a mutant, in which all SCPs were additionally deleted. Depletion of SCPs led to structural rearrangements in Photosystem II (PSII): less photosystems were assembled; and in these, the Q(B) site was modified. Despite the lower amount of PSII, the SCP-deficient cells contained the same amount of phycobilisomes (PBS) as the control. Although the excess PBS were functionally disconnected, their fluorescence was quenched under high irradiance by the activated Orange Carotenoid Protein (OCP). Additionally the amount of OCP, but not of the iron-stress induced protein (isiA), was higher in this SCP-depleted mutant compared with the control. As previously described, the lack of SCPs affects the chlorophyll biosynthesis (Vavilin, D., Brune, D. C., Vermaas, W. (2005) Biochim Biophys Acta 1708, 91-101). We demonstrate that chlorophyll synthesis is required for efficient PSII repair and that it is partly impaired in the absence of SCPs. At the same time, the amount of chlorophyll also seems to influence the expression of ScpC and ScpD.
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21
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Funk C, Alami M, Tibiletti T, Green BR. High light stress and the one-helix LHC-like proteins of the cryptophyte Guillardia theta. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:841-6. [PMID: 21459077 DOI: 10.1016/j.bbabio.2011.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 03/23/2011] [Accepted: 03/24/2011] [Indexed: 10/18/2022]
Abstract
Cryptophytes like the cryptomonad Guillardia theta are part of the marine phytoplankton and therefore major players in global carbon and biogeochemical cycles. Despite the importance for the cell in being able to cope with large changes in illumination on a daily basis, very little is known about photoprotection mechanisms in cryptophytes. Here, we show that Guillardia theta is able to perform non-photochemical quenching, although none of the usual xanthophyll cycle pigments (e.g., zeaxanthin, diadinoxanthin, diatoxanthin) are present at detectable levels. Instead, acclimation to high light intensity seems to involve an increase of alloxanthin. Guillardia theta has genes for 2 one-helix "light-harvesting-like" proteins, related to some cyanobacterial genes which are induced in response to high light stress. Both the plastid-encoded gene (hlipP) and the nucleomorph-encoded gene (HlipNm) are expressed, but transcript levels decrease rather than increase during high light exposure, suggesting that they are not involved in a high light stress response. The HlipNm protein was detected with a specific antibody; expression was constant, independent of the light exposure.
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Affiliation(s)
- Christiane Funk
- Department of Chemistry, Umeå University, S-90187 Umeå, Sweden.
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22
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Neilson JAD, Durnford DG. Structural and functional diversification of the light-harvesting complexes in photosynthetic eukaryotes. PHOTOSYNTHESIS RESEARCH 2010; 106:57-71. [PMID: 20596891 DOI: 10.1007/s11120-010-9576-2] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 06/16/2010] [Indexed: 05/25/2023]
Abstract
Eukaryotes acquired photosynthetic metabolism over a billion years ago, and during that time the light-harvesting antennae have undergone significant structural and functional divergence. The antenna systems are generally used to harvest and transfer excitation energy into the reaction centers to drive photosynthesis, but also have the dual role of energy dissipation. Phycobilisomes formed the first antenna system in oxygenic photoautotrophs, and this soluble protein complex continues to be the dominant antenna in extant cyanobacteria, glaucophytes, and red algae. However, phycobilisomes were lost multiple times during eukaryotic evolution in favor of a thylakoid membrane-integral light-harvesting complex (LHC) antenna system found in the majority of eukaryotic taxa. While photosynthesis spread across different eukaryotic kingdoms via endosymbiosis, the antenna systems underwent extensive modification as photosynthetic groups optimized their light-harvesting capacity and ability to acclimate to changing environmental conditions. This review discusses the different classes of LHCs within photosynthetic eukaryotes and examines LHC diversification in different groups in a structural and functional context.
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Affiliation(s)
- Jonathan A D Neilson
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
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23
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Neilson JA, Durnford DG. Evolutionary distribution of light-harvesting complex-like proteins in photosynthetic eukaryotes. Genome 2010; 53:68-78. [DOI: 10.1139/g09-081] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Light-harvesting-like (LIL) proteins are low-molecular-mass membrane proteins related to the light-harvesting complexes, which form the dominant antenna system in most photosynthetic eukaryotes. To analyze the LIL protein family, we mined a number of publicly available databases to identify members of this family in a broad range of organisms. LIL proteins are diverse, having one to three predicted transmembrane helices. One- and two-helix LIL proteins were found in all the major photosynthetic eukaryote lineages (glaucophytes, red algae, and green algae) and are particularly well conserved in the green algae and land plants. In most cases, however, these proteins are not conserved between major lineages, and in some cases appear to have evolved independently. Three-helix LIL proteins are well conserved within the gymnosperms and angiosperms, but are much more divergent, and have been duplicated multiple times, in the green algae and bryophytes. We also identified a novel LIL protein in two Micromonas strains that contains a fourth hydrophobic region. This analysis identifies conserved members of the LIL protein family, signifying their importance to photosynthetic eukaryotes. It also indicates that classification of these proteins based on structural characteristics alone inadequately reflects the evolutionary history observed in this complex protein family.
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Affiliation(s)
| | - Dion G. Durnford
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
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