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Sepúlveda-Espinoza F, Cofré-Serrano A, Veloso-Valeria T, Quesada-Calderon S, Guillemin ML. Characterization of the organellar genomes of Mazzaella laminarioides and Mazaella membranacea (Gigartinaceae, Rhodophyta). JOURNAL OF PHYCOLOGY 2024. [PMID: 38944824 DOI: 10.1111/jpy.13478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/08/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024]
Abstract
Mazzaella, a genus with no genomic resources available, has extensive distribution in the cold waters of the Pacific, where they represent ecologically and economically important species. In this study, we aimed to sequence, assemble, and annotate the complete mitochondrial and chloroplast genomes from two Mazzaella spp. and characterize the intraspecific variation among them. We report for the first time seven whole organellar genomes (mitochondria: OR915856, OR947465, OR947466, OR947467, OR947468, OR947469, OR947470; chloroplast: OR881974, OR909680, OR909681, OR909682, OR909683, OR909684, OR909685) obtained through high-throughput sequencing for six M. laminarioides sampled from three Chilean regions and one M. membranacea. Sequenced Mazzaella mitogenomes have identical gene number, gene order, and genome structure. The same results were observed for assembled plastomes. A total of 52 genes were identified in mitogenomes, and a total of 235 genes were identified in plastomes. Although the M. membranacea plastome included a full-length pbsA gene, in all M. laminarioides samples, the pbsA gene was split in three open reading frames (ORFs). Within M. laminarioides, we observed important plastome lineage-specific variations, such as the pseudogenization of the two hypothetical protein-coding genes, ycf23 and ycf45. Nonsense mutations in the ycf23 and ycf45 genes were only detected in the northern lineage. These results are consistent with phylogenetic reconstructions and divergence time estimation using concatenated coding sequences that not only support the monophyly of M. laminarioides but also underscore that the three M. laminarioides lineages are in an advanced stage of divergence. These new results open the question of the existence of still undisclosed species in M. laminarioides.
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Affiliation(s)
- Francisco Sepúlveda-Espinoza
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Laboratorio de Epigenética Vegetal, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, Chile
| | - Angela Cofré-Serrano
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Tomás Veloso-Valeria
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Suany Quesada-Calderon
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- AUSTRAL-Omics, Vicerrectoría de Investigación, desarrollo y creación artística (VIDCA), Universidad Austral de Chile, Valdivia, Chile
| | - Marie-Laure Guillemin
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Núcleo Milenio MASH, Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
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Singh N, Bhatla SC. Heme oxygenase-nitric oxide crosstalk-mediated iron homeostasis in plants under oxidative stress. Free Radic Biol Med 2022; 182:192-205. [PMID: 35247570 DOI: 10.1016/j.freeradbiomed.2022.02.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 12/22/2022]
Abstract
Plant growth under abiotic stress conditions significantly enhances intracellular generation of reactive oxygen species (ROS). Oxidative status of plant cells is directly affected by the modulation of iron homeostasis. Among mammals and plants, heme oxygenase-1 (HO-1) is a well-known antioxidant enzyme. It catalyzes oxygenation of heme, thereby producing Fe2+, CO and biliverdin as byproducts. The antioxidant potential of HO-1 is primarily due to its catalytic reaction byproducts. Biliverdin and bilirubin possess conjugated π-electrons which escalate the ability of these biomolecules to scavenge free radicals. CO also enhances the ROS scavenging ability of plants cells by upregulating catalase and peroxidase activity. Enhanced expression of HO-1 in plants under oxidative stress accompanies sequestration of iron in specialized iron storage proteins localized in plastids and mitochondria, namely ferritin for Fe3+ storage and frataxin for storage of Fe-S clusters, respectively. Nitric oxide (NO) crosstalks with HO-1 at multiple levels, more so in plants under oxidative stress, in order to maintain intracellular iron status. Formation of dinitrosyl-iron complexes (DNICs) significantly prevents Fenton reaction during oxidative stress. DNICs also release NO upon dissociation in target cells over long distance in plants. They also function as antioxidants against superoxide anions and lipidic free radicals. A number of NO-modulated transcription factors also facilitate iron homeostasis in plant cells. Plants facing oxidative stress exhibit modulation of lateral root formation by HO-1 through NO and auxin-dependent pathways. The present review provides an in-depth analysis of the structure-function relationship of HO-1 in plants and mammals, correlating them with their adaptive mechanisms of survival under stress.
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Affiliation(s)
- Neha Singh
- Department of Botany, Gargi College, University of Delhi, India.
| | - Satish C Bhatla
- Laboratory of Plant Physiology and Biochemistry, Department of Botany, University of Delhi, Delhi, 110007, India.
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Zheng T, Wang M, Zhan J, Sun W, Yang Q, Lin Z, Bu T, Tang Z, Li C, Yan J, Shan Z, Chen H. Ferrous iron-induced increases in capitate glandular trichome density and upregulation of CbHO-1 contributes to increases in blinin content in Conyza blinii. PLANTA 2020; 252:81. [PMID: 33037484 DOI: 10.1007/s00425-020-03492-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
Ferrous iron can promote the development of glandular trichomes and increase the content of blinin, which depends on CbHO-1 expression. Conyza blinii (C. blinii) is a unique Chinese herbal medicine that grows in Sichuan Province, China. Because the habitat of C. blinii is an iron ore mining area with abundant iron content, this species can be used as one of the best materials to study the mechanism of plant tolerance to iron. In this study, C. blinii was treated with ferrous-EDTA solutions at different concentrations, and it was found that the tolerance value of C. blinii to iron was 200 μM. Under this concentration, the plant height, root length, biomass, and iron content of C. blinii increased to the maximum values, and the effect was dependent on the upregulated expression of CbHO-1. At the same time, under ferrous iron, the photosynthetic capacity and capitate glandular trichome density of C. blinii also significantly increased, providing precursors and sites for the synthesis of blinin, thus significantly increasing the content of blinin. These processes were also dependent on the high expression of CbHO-1. Correlation analysis showed that there were strong positive correlations between iron content, capitate glandular trichome density, CbHO-1 gene expression, and blinin content. This study explored the effects of ferrous iron on the physiology and biochemistry of C. blinii, greatly improving our understanding of the mechanism of iron tolerance in C. blinii.
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Affiliation(s)
- Tianrun Zheng
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Maojia Wang
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Junyi Zhan
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Wenjun Sun
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Qin Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Zhiyi Lin
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Tongliang Bu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Zizhong Tang
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Jun Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture Rural Affairs, School of Food and Bioengineering, Chengdu University, Chengdu, China
| | - Zhi Shan
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya'an, China.
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Cho CH, Choi JW, Lam DW, Kim KM, Yoon HS. Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats. PLoS One 2018; 13:e0196995. [PMID: 29738547 PMCID: PMC5940233 DOI: 10.1371/journal.pone.0196995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/24/2018] [Indexed: 01/03/2023] Open
Abstract
The red algal subclass Nemaliophycidae includes both marine and freshwater taxa that contribute to more than half of the freshwater species in Rhodophyta. Given that these taxa inhabit diverse habitats, the Nemaliophycidae is a suitable model for studying environmental adaptation. For this purpose, we characterized plastid genomes of two freshwater species, Kumanoa americana (Batrachospermales) and Thorea hispida (Thoreales), and one marine species Palmaria palmata (Palmariales). Comparative genome analysis identified seven genes (ycf34, ycf35, ycf37, ycf46, ycf91, grx, and pbsA) that were different among marine and freshwater species. Among currently available red algal plastid genomes (127), four genes (pbsA, ycf34, ycf35, ycf37) were retained in most of the marine species. Among these, the pbsA gene, known for encoding heme oxygenase, had two additional copies (HMOX1 and HMOX2) that were newly discovered and were reported from previously red algal nuclear genomes. Each type of heme oxygenase had a different evolutionary history and special modifications (e.g., plastid targeting signal peptide). Based on this observation, we suggest that the plastid-encoded pbsA contributes to the iron controlling system in iron-deprived conditions. Thus, we highlight that this functional requirement may have prevented gene loss during the long evolutionary history of red algal plastid genomes.
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Affiliation(s)
- Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Daryl W. Lam
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Kyeong Mi Kim
- Marine Biodiversity Institute of Korea, Seocheon, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
- * E-mail:
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Manirafasha E, Murwanashyaka T, Ndikubwimana T, Rashid Ahmed N, Liu J, Lu Y, Zeng X, Ling X, Jing K. Enhancement of cell growth and phycocyanin production in Arthrospira (Spirulina) platensis by metabolic stress and nitrate fed-batch. BIORESOURCE TECHNOLOGY 2018; 255:293-301. [PMID: 29422330 DOI: 10.1016/j.biortech.2017.12.068] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 06/08/2023]
Abstract
Arthrospira (Spirulina) platensis is known to have high-quality proteins content and phycocyanin as one of the major pigment constituents of the cells, and the most challenging problem associated with phycocyanin production in Arthrospira is to optimize its intracellular accumulation. The present study evaluated the metabolic stress conditions (by nutrient enrichment) of Arthrospira platensis FACHB-314 for boosting biomass growth and high content phycocyanin accumulation. Experimental results showed that 5 mM sodium glutamate and 7.5 mM succinic acid could enhance biomass yield as well as phycocyanin accumulation compared with that of the control groups. The present study demonstrates that the biomass growth and phycocyanin accumulation were significantly enhanced in fed-batch cultivation of Arthrospira platensis by applying the substrates as metabolic stress agents combined with nitrate feeding strategy. cobA/hemD, hemG and ho genes presented the over-expression level with adding sodium glutamate and succinic acid in cultures, respectively, compared to the control groups.
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Affiliation(s)
- Emmanuel Manirafasha
- Department of Chemical and Biochemical Engineering and the Key Lab for Synthetic Biotechnology of Xiamen City, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; University of Rwanda-College of Education, P.O. Box 5039, Kigali, Rwanda
| | - Theophile Murwanashyaka
- Department of Chemical and Biochemical Engineering and the Key Lab for Synthetic Biotechnology of Xiamen City, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | | | - Nur Rashid Ahmed
- Department of Chemical and Biochemical Engineering and the Key Lab for Synthetic Biotechnology of Xiamen City, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jingyi Liu
- Department of Chemical and Biochemical Engineering and the Key Lab for Synthetic Biotechnology of Xiamen City, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yinghua Lu
- Department of Chemical and Biochemical Engineering and the Key Lab for Synthetic Biotechnology of Xiamen City, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Xianhai Zeng
- College of Energy, Xiamen University, Xiamen 361005, China
| | - Xueping Ling
- Department of Chemical and Biochemical Engineering and the Key Lab for Synthetic Biotechnology of Xiamen City, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Keju Jing
- Department of Chemical and Biochemical Engineering and the Key Lab for Synthetic Biotechnology of Xiamen City, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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Mahawar L, Shekhawat GS. Haem oxygenase: A functionally diverse enzyme of photosynthetic organisms and its role in phytochrome chromophore biosynthesis, cellular signalling and defence mechanisms. PLANT, CELL & ENVIRONMENT 2018; 41:483-500. [PMID: 29220548 DOI: 10.1111/pce.13116] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/26/2017] [Accepted: 11/23/2017] [Indexed: 05/08/2023]
Abstract
Haem oxygenase (HO) is a universal enzyme that catalyses stereospecific cleavage of haem to BV IX α and liberates Fe+2 ion and CO as by-product. Beside haem degradation, it has important functions in plants that include cellular defence, stomatal regulation, iron mobilization, phytochrome chromophore synthesis, and lateral root formation. Phytochromes are an extended family of photoreceptors with a molecular mass of 250 kDa and occur as a dimer made up of 2 equivalent subunits of 125 kDa each. Each subunit is made of two components: the chromophore, a light-capturing pigment molecule and the apoprotein. Biosynthesis of phytochrome (phy) chromophore includes the oxidative splitting of haem to biliverdin IX by an enzyme HO, which is the decisive step in the biosynthesis. In photosynthetic organisms, BVα is reduced to 3Z PΦB by a ferredoxin-dependent PΦB synthase that finally isomerised to PΦB. The synthesized PΦB assembles with the phytochrome apoprotein in the cytoplasm to generate holophytochrome. Thus, necessary for photomorphogenesis in plants, which has confirmed from the genetic studies, conducted on Arabidopsis thaliana and pea. Besides the phytochrome chromophore synthesis, the review also emphasises on the current advances conducted in plant HO implying its developmental and defensive role.
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Affiliation(s)
- Lovely Mahawar
- Department of Botany, Jai Narain Vyas University, Jodhpur, 342001, India
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7
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Muñoz-Gómez SA, Mejía-Franco FG, Durnin K, Colp M, Grisdale CJ, Archibald JM, Slamovits CH. The New Red Algal Subphylum Proteorhodophytina Comprises the Largest and Most Divergent Plastid Genomes Known. Curr Biol 2017; 27:1677-1684.e4. [DOI: 10.1016/j.cub.2017.04.054] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 12/25/2022]
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8
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Ledermann B, Béjà O, Frankenberg-Dinkel N. New biosynthetic pathway for pink pigments from uncultured oceanic viruses. Environ Microbiol 2016; 18:4337-4347. [PMID: 26950653 DOI: 10.1111/1462-2920.13290] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/04/2016] [Indexed: 12/18/2022]
Abstract
The pink open-chain tetrapyrrole pigment phycoerythrobilin (PEB) is employed by marine cyanobacteria, red algae and cryptophytes as a light-harvesting chromophore in phycobiliproteins. Genes encoding biosynthesis proteins for PEB have also been discovered in cyanophages, viruses that infect cyanobacteria, and mimic host pigment biosynthesis with the exception of PebS which combines the enzymatic activities of two host enzymes. In this study, we have identified novel members of the PEB biosynthetic enzyme families, heme oxygenases and ferredoxin-dependent bilin reductases. Encoding genes were found in metagenomic datasets and could be traced back to bacteriophage but not cyanophage origin. While the heme oxygenase exhibited standard activity, a new bilin reductase with highest homology to the teal pigment producing enzyme PcyA revealed PEB biosynthetic activity. Although PcyX possesses PebS-like activity both enzymes share only 9% sequence identity and likely catalyze the reaction via two independent mechanisms. Our data point towards the presence of phycobilin biosynthetic genes in phages that probably infect alphaproteobacteria and, therefore, further support a role of phycobilins outside oxygenic phototrophs.
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Affiliation(s)
- Benjamin Ledermann
- Department of Biology, Microbiology, Technical University Kaiserslautern, Kaiserslautern, Germany
| | - Oded Béjà
- Technion-Israel Institute of Technology, Haifa, Israel
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Hernández-Prieto MA, Semeniuk TA, Giner-Lamia J, Futschik ME. The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803. Sci Rep 2016; 6:22168. [PMID: 26923200 PMCID: PMC4770689 DOI: 10.1038/srep22168] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/09/2016] [Indexed: 01/03/2023] Open
Abstract
Cyanobacteria exhibit a great capacity to adapt to different environmental conditions through changes in gene expression. Although this plasticity has been extensively studied in the model cyanobacterium Synechocystis sp. PCC 6803, a detailed analysis of the coordinated transcriptional adaption across varying conditions is lacking. Here, we report a meta-analysis of 756 individual microarray measurements conducted in 37 independent studies-the most comprehensive study of the Synechocystis transcriptome to date. Using stringent statistical evaluation, we characterized the coordinated adaptation of Synechocystis' gene expression on systems level. Evaluation of the data revealed that the photosynthetic apparatus is subjected to greater changes in expression than other cellular components. Nevertheless, network analyses indicated a significant degree of transcriptional coordination of photosynthesis and various metabolic processes, and revealed the tight co-regulation of components of photosystems I, II and phycobilisomes. Detailed inspection of the integrated data led to the discovery a variety of regulatory patterns and novel putative photosynthetic genes. Intriguingly, global clustering analyses suggested contrasting transcriptional response of metabolic and regulatory genes stress to conditions. The integrated Synechocystis transcriptome can be accessed and interactively analyzed via the CyanoEXpress website (http://cyanoexpress.sysbiolab.eu).
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Affiliation(s)
- Miguel A. Hernández-Prieto
- Systems Biology and Bioinformatics Laboratory, Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - Trudi Ann Semeniuk
- Systems Biology and Bioinformatics Laboratory, Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - Joaquín Giner-Lamia
- Systems Biology and Bioinformatics Laboratory, Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - Matthias E. Futschik
- Systems Biology and Bioinformatics Laboratory, Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
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Nitric oxide and iron modulate heme oxygenase activity as a long distance signaling response to salt stress in sunflower seedling cotyledons. Nitric Oxide 2016; 53:54-64. [DOI: 10.1016/j.niox.2016.01.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/30/2015] [Accepted: 01/11/2016] [Indexed: 12/11/2022]
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Heme-iron utilization by Leptospira interrogans requires a heme oxygenase and a plastidic-type ferredoxin-NADP+ reductase. Biochim Biophys Acta Gen Subj 2014; 1840:3208-17. [PMID: 25092651 DOI: 10.1016/j.bbagen.2014.07.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/04/2014] [Accepted: 07/28/2014] [Indexed: 11/24/2022]
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Li H, Song JB, Zhao WT, Yang ZM. AtHO1 is Involved in Iron Homeostasis in an NO-Dependent Manner. ACTA ACUST UNITED AC 2013; 54:1105-17. [DOI: 10.1093/pcp/pct063] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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13
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Janouškovec J, Liu SL, Martone PT, Carré W, Leblanc C, Collén J, Keeling PJ. Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers. PLoS One 2013; 8:e59001. [PMID: 23536846 PMCID: PMC3607583 DOI: 10.1371/journal.pone.0059001] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 02/08/2013] [Indexed: 11/21/2022] Open
Abstract
Red algae have the most gene-rich plastid genomes known, but despite their evolutionary importance these genomes remain poorly sampled. Here we characterize three complete and one partial plastid genome from a diverse range of florideophytes. By unifying annotations across all available red algal plastid genomes we show they all share a highly compact and slowly-evolving architecture and uniquely rich gene complements. Both chromosome structure and gene content have changed very little during red algal diversification, and suggest that plastid-to nucleus gene transfers have been rare. Despite their ancient character, however, the red algal plastids also contain several unprecedented features, including a group II intron in a tRNA-Met gene that encodes the first example of red algal plastid intron maturase – a feature uniquely shared among florideophytes. We also identify a rare case of a horizontally-acquired proteobacterial operon, and propose this operon may have been recruited for plastid function and potentially replaced a nucleus-encoded plastid-targeted paralogue. Plastid genome phylogenies yield a fully resolved tree and suggest that plastid DNA is a useful tool for resolving red algal relationships. Lastly, we estimate the evolutionary rates among more than 200 plastid genes, and assess their usefulness for species and subspecies taxonomy by comparison to well-established barcoding markers such as cox1 and rbcL. Overall, these data demonstrates that red algal plastid genomes are easily obtainable using high-throughput sequencing of total genomic DNA, interesting from evolutionary perspectives, and promising in resolving red algal relationships at evolutionarily-deep and species/subspecies levels.
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Affiliation(s)
- Jan Janouškovec
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
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Chen D, Brown JD, Kawasaki Y, Bommer J, Takemoto JY. Scalable production of biliverdin IXα by Escherichia coli. BMC Biotechnol 2012; 12:89. [PMID: 23176158 PMCID: PMC3534565 DOI: 10.1186/1472-6750-12-89] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/04/2012] [Indexed: 01/16/2023] Open
Abstract
Background Biliverdin IXα is produced when heme undergoes reductive ring cleavage at the α-methene bridge catalyzed by heme oxygenase. It is subsequently reduced by biliverdin reductase to bilirubin IXα which is a potent endogenous antioxidant. Biliverdin IXα, through interaction with biliverdin reductase, also initiates signaling pathways leading to anti-inflammatory responses and suppression of cellular pro-inflammatory events. The use of biliverdin IXα as a cytoprotective therapeutic has been suggested, but its clinical development and use is currently limited by insufficient quantity, uncertain purity, and derivation from mammalian materials. To address these limitations, methods to produce, recover and purify biliverdin IXα from bacterial cultures of Escherichia coli were investigated and developed. Results Recombinant E. coli strains BL21(HO1) and BL21(mHO1) expressing cyanobacterial heme oxygenase gene ho1 and a sequence modified version (mho1) optimized for E. coli expression, respectively, were constructed and shown to produce biliverdin IXα in batch and fed-batch bioreactor cultures. Strain BL21(mHO1) produced roughly twice the amount of biliverdin IXα than did strain BL21(HO1). Lactose either alone or in combination with glycerol supported consistent biliverdin IXα production by strain BL21(mHO1) (up to an average of 23. 5mg L-1 culture) in fed-batch mode and production by strain BL21 (HO1) in batch-mode was scalable to 100L bioreactor culture volumes. Synthesis of the modified ho1 gene protein product was determined, and identity of the enzyme reaction product as biliverdin IXα was confirmed by spectroscopic and chromatographic analyses and its ability to serve as a substrate for human biliverdin reductase A. Conclusions Methods for the scalable production, recovery, and purification of biliverdin IXα by E. coli were developed based on expression of a cyanobacterial ho1 gene. The purity of the produced biliverdin IXα and its ability to serve as substrate for human biliverdin reductase A suggest its potential as a clinically useful therapeutic.
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Affiliation(s)
- Dong Chen
- Synthetic Bioproducts Center, 620 North 600 East, Utah State University, North Logan, Utah 84341, USA.
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15
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Gisk B, Wiethaus J, Aras M, Frankenberg-Dinkel N. Variable composition of heme oxygenases with different regiospecificities in Pseudomonas species. Arch Microbiol 2012; 194:597-606. [DOI: 10.1007/s00203-012-0796-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 01/13/2012] [Accepted: 01/20/2012] [Indexed: 01/20/2023]
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16
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Shen Q, Jiang M, Li H, Che LL, Yang ZM. Expression of a Brassica napus heme oxygenase confers plant tolerance to mercury toxicity. PLANT, CELL & ENVIRONMENT 2011; 34:752-63. [PMID: 21241331 DOI: 10.1111/j.1365-3040.2011.02279.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant heme oxygenases (HOs) regulate biosynthesis of phytochrome which accounts for photo-acceptance and -morphogenesis. Recent studies have demonstrated that plant HOs also regulate many other physiological processes including response to environmental stimuli. To elucidate the mechanism by which HOs regulate plant adaptation to heavy metal exposure, three novel HOs genes were isolated from rapeseed (Brassica napus) and their expression patterns were analysed. Alignment of deduced protein sequences revealed that the three BnHOs share high identity with their corresponding orthologos (AtHO1-3) from Arabidopsis. To investigate whether the BnHO regulates plant tolerance to Hg toxicity, we constructed B. napus transgenic plants overexpressing BnHO-1. Under Hg stress, the transgenic plants had 1.41-1.59 folds higher biomass than the untransformants. However, overexpression of BnHO-1 resulted in less accumulation of Hg in some lines of transformants than in untransformants. The transgenic plants show lower abundance of reactive oxygen species and attenuated oxidative injury compared with the untransgenic plants. We cloned the promoter sequences of BnHO-1 from B. napus. Analysis revealed that the 1119 bp fragment contains a conserved Cd responsive element (CdRE) and others responding to multiple environmental stimuli. Transient expression in tobacco leaves showed differential responses to heavy metals (Zn, Cu, Pb, Hg and Cd).
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Affiliation(s)
- Qi Shen
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
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Shekhawat GS, Verma K. Haem oxygenase (HO): an overlooked enzyme of plant metabolism and defence. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:2255-70. [PMID: 20378668 DOI: 10.1093/jxb/erq074] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Haem oxygenase (HO) degrades free haem released from haem proteins with the generation of ferrous iron (Fe2+), biliverdin-IXalpha (BV-IXalpha), and carbon monoxide (CO). The mechanism of haem cleavage has been conserved between plants and other organisms even though the function, subcellular localization, and cofactor requirements of HO differ substantially. The crystal structure of HO1, a monomeric protein, has been extensively reported in mammals, pathogenic bacteria, and cyanobacteria, but no such reports are available for higher plant HOs except a predicted model for pea HO1. Along with haem degradation, HO performs various cellular processes including iron acquisition/mobilization, phytochrome chromophore synthesis, cell protection, and stomatal regulation. To date, four HO genes (HO1, HO2, HO3, and HO4) have been reported in plants. HO1 has been well explored in cell metabolism; however, the divergent roles of the other three HOs is less known. The transcriptional up-regulation of HO1 in plants responds to many agents, such as light, UV, iron deprivation, reactive oxygen species (ROS), abscisic acid (ABA), and haematin. Recently the HO1/CO system has gained more attention due to its physiological cytoprotective role in plants. This review focuses on the recent advances made in plant HO research involving its role in environmental stresses. Moreover, the review emphasizes physiological, biochemical, and molecular aspects of this enzyme in plants.
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Affiliation(s)
- G S Shekhawat
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali-304022, Rajasthan, India.
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Abstract
In eukaryotes, RNA trans-splicing is an important RNA-processing form for the end-to-end ligation of primary transcripts that are derived from separately transcribed exons. So far, three different categories of RNA trans-splicing have been found in organisms as diverse as algae to man. Here, we review one of these categories: the trans-splicing of discontinuous group II introns, which occurs in chloroplasts and mitochondria of lower eukaryotes and plants. Trans-spliced exons can be predicted from DNA sequences derived from a large number of sequenced organelle genomes. Further molecular genetic analysis of mutants has unravelled proteins, some of which being part of high-molecular-weight complexes that promote the splicing process. Based on data derived from the alga Chlamydomonas reinhardtii, a model is provided which defines the composition of an organelle spliceosome. This will have a general relevance for understanding the function of RNA-processing machineries in eukaryotic organelles.
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Affiliation(s)
- Stephanie Glanz
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
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Okada K. The novel heme oxygenase-like protein fromPlasmodiumfalciparumconverts heme to bilirubin IXα in the apicoplast. FEBS Lett 2008; 583:313-9. [DOI: 10.1016/j.febslet.2008.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 12/02/2008] [Accepted: 12/05/2008] [Indexed: 11/24/2022]
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Guo K, Xia K, Yang ZM. Regulation of tomato lateral root development by carbon monoxide and involvement in auxin and nitric oxide. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:3443-52. [PMID: 18653694 PMCID: PMC2529230 DOI: 10.1093/jxb/ern194] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 06/24/2008] [Accepted: 07/01/2008] [Indexed: 05/20/2023]
Abstract
Carbon monoxide (CO) is an endogenous gaseous molecule in organisms. Despite its reputation as a lethal gas, recent studies have shown that it is one of the most essential cellular components regulating a variety of biological processes. However, whether CO regulates physiological processes of morphological or developmental patterns in plants is largely unknown. In this paper, the observation that exogenous CO was able to promote the formation of tomato lateral roots (LR) is described. The CO stimulation of LR development was supported by analysis of tomato haem oxygenase-1 (LeHO-1), an enzymatic source of intracellular CO. It is shown that the amount of LeHO-1 proteins and transcripts increased parallel to the LR development. In addition, LeHO-1 loss-of-function tomato mutant yg-2 showed a phenotype of impaired LR development. The phenotype of yg-2 could be restored by treatment with CO. Since auxin is required for LR initiation and NO is shown to be a mediator for LR development, the correlation of CO with auxin and NO was tested. Our analysis revealed that the action of CO was blocked by the auxin transport inhibitor N-1-naphthylphthalamic acid and the NO scavenger cPTIO, respectively. Furthermore, the whole seedling assays of IAA show that treatment with CO increased the overall IAA levels in various tissues of tomato. Exposure of tomato roots to CO also enhanced intracellular NO generation. These results indicate that CO plays a critical role in controlling architectural change in tomato roots.
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Affiliation(s)
- Kai Guo
- Department of Biochemistry and Molecular Biology, College of Life Science, Weigang No. 1, Outside the Zhongshan Men, Building of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Xia
- Department of Plant Science, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Weigang No. 1, Outside the Zhongshan Men, Building of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
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Dammeyer T, Frankenberg-Dinkel N. Function and distribution of bilin biosynthesis enzymes in photosynthetic organisms. Photochem Photobiol Sci 2008; 7:1121-30. [PMID: 18846276 DOI: 10.1039/b807209b] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bilins are open-chain tetrapyrrole molecules essential for light-harvesting and/or sensing in many photosynthetic organisms. While they serve as chromophores in phytochrome-mediated light-sensing in plants, they additionally function in light-harvesting in cyanobacteria, red algae and cryptomonads. Associated to phycobiliproteins a variety of bile pigments is responsible for the specific light-absorbance properties of the organisms enabling efficient photosynthesis under different light conditions. The initial step of bilin biosynthesis is the cleavage of heme by heme oxygenases (HO) to afford the first linear molecule biliverdin. This reaction is ubiquitously found also in non-photosynthetic organisms. Biliverdin is then further reduced by site specific reductases most of them belonging to the interesting family of ferredoxin-dependent bilin reductases (FDBRs)-a new family of radical oxidoreductases. In recent years much progress has been made in the field of heme oxygenases but even more in the widespread family of FDBRs, revealing novel biochemical FDBR activities, new crystal structures and new ecological aspects, including the discovery of bilin biosynthesis genes in wild marine phage populations. The aim of this review is to summarize and discuss the recent progress in this field and to highlight the new and remaining questions.
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Affiliation(s)
- Thorben Dammeyer
- Physiology of Microorganisms, Ruhr-University Bochum, Universitaetsstr. 150, 44780 Bochum, Germany
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22
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Heme oxygenase-1 polymorphism associated with severity of chronic obstructive pulmonary disease. Chin Med J (Engl) 2007. [DOI: 10.1097/00029330-200701010-00003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Yannarelli GG, Noriega GO, Batlle A, Tomaro ML. Heme oxygenase up-regulation in ultraviolet-B irradiated soybean plants involves reactive oxygen species. PLANTA 2006; 224:1154-62. [PMID: 16703357 DOI: 10.1007/s00425-006-0297-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Accepted: 04/17/2006] [Indexed: 05/04/2023]
Abstract
Ultraviolet-B (UV-B) radiation has a negative impact on plant cells, and leads to the generation of reactive oxygen species (ROS). Heme oxygenase (HO, EC 1.14.99.3) plays a protective role against oxidative stress in mammals, but little is known about this issue in plants. Here, we report for the first time the response of HO in leaves of soybean (Glycine max L.) plants subjected to UV-B radiation. Under 7.5 and 15 kJ m(-2 )UV-B doses, HO, catalase (CAT, EC 1.11.1.6) and ascorbate peroxidase (APX, EC 1.11.1.11) activities were increased and the production of thiobarbituric acid reactive substances (TBARS) regain control values after 4 h of plant recuperation. Treatment with 30 kJ m(-2) UV-B provoked a decrease in these antioxidant enzyme activities. Immunoblot analysis showed a 4.3 and 3.7-fold increase in HO-1 protein expression after irradiation with 7.5 and 15 kJ m(-2), respectively. HO-1 transcript levels were enhanced (up to 77%) at these doses, as assessed by semi-quantitative RT-PCR. These data demonstrated that increased HO activity was associated with augmented protein expression and transcript levels. Plants pre-treated with the antioxidant ascorbic acid did not show the UV-B-induced up-regulation of HO-1 mRNA, but hydrogen peroxide treatment could mimic this reaction. Our results indicate that HO is up-regulated in a dose-depending manner as a mechanism of cell protection against oxidative damage and that such response occurred as a consequence of HO-1 mRNA enhancement involving ROS.
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Affiliation(s)
- Gustavo G Yannarelli
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina.
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Abstract
The importance of heme oxygenases in heme catabolism, iron utilization, and cellular signaling has been recognized for many years and is a well studied process in eukaryotes. Through the accessibility of an increasing number of bacterial genomes, it has become evident that heme oxygenases are also widespread in prokaryotes. In these organisms, the heme oxygenase reaction serves a similar function as in eukaryotes. A major role of bacterial heme oxygenases has been attributed to acquisition of iron in prokaryotic pathogens, but other functions, such as involvement in phytobilin biosynthesis, have been described. This review summarizes the current state of the art on bacterial heme oxygenase research. The various biological roles of this enzyme in prokaryotes and their biochemical properties will be discussed.
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Zhang X, Sato M, Sasahara M, Migita CT, Yoshida T. Unique features of recombinant heme oxygenase of Drosophila melanogaster compared with those of other heme oxygenases studied. ACTA ACUST UNITED AC 2004; 271:1713-24. [PMID: 15096210 DOI: 10.1111/j.1432-1033.2004.04077.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We cloned a cDNA for a Drosophila melanogaster homologue of mammalian heme oxygenase (HO) and constructed a bacterial expression system of a truncated, soluble form of D. melanogaster HO (DmDeltaHO). The purified DmDeltaHO degraded hemin to biliverdin, CO and iron in the presence of reducing systems such as NADPH/cytochrome P450 reductase and sodium ascorbate, although the reaction rate was slower than that of mammalian HOs. Some properties of DmHO, however, are quite different from other known HOs. Thus DmDeltaHO bound hemin stoichiometrically to form a hemin-enzyme complex like other HOs, but this complex did not show an absorption spectrum of hexa-coordinated heme protein. The absorption spectrum of the ferric complex was not influenced by changing the pH of the solution. Interestingly, an EPR study revealed that the iron of heme was not involved in binding heme to the enzyme. Hydrogen peroxide failed to convert it into verdoheme. A spectrum of the ferrous-CO form of verdoheme was not detected during the reaction from hemin under oxygen and CO. Degradation of hemin catalyzed by DmDeltaHO yielded three isomers of biliverdin, of which biliverdin IXalpha and two other isomers (IXbeta and IXdelta) accounted for 75% and 25%, respectively. Taken together, we conclude that, although DmHO acts as a real HO in D. melanogaster, its active-site structure is quite different from those of other known HOs.
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Affiliation(s)
- Xuhong Zhang
- Department of Biochemistry, Yamagata University School of Medicine, Japan
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Desquilbet TE, Duval JC, Robert B, Houmard J, Thomas JC. In the Unicellular Red Alga Rhodella violacea Iron Deficiency Induces an Accumulation of Uncoupled LHC. ACTA ACUST UNITED AC 2003; 44:1141-51. [PMID: 14634150 DOI: 10.1093/pcp/pcg139] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Iron plays a key role in the synthesis and functioning of the photosynthetic apparatus. Conditions of partial iron deficiency that lead to a relatively stable phenotype were established and the effects of starvation studied in the unicellular red alga, Rhodella violacea. Synthesis of the photosynthetic pigments were found to decrease, with phycobiliproteins being affected to a lesser extent than chlorophyll a. Biophysical, biochemical and immunological approaches were used to show that the PSI content is highly diminished and the PSII/PSI stoichiometry increased by a factor of 5 compared to standard conditions. Meanwhile light-harvesting complex (LHC) was still assembled in the thylakoid membranes at unchanged levels. The use of translation inhibitors for either nuclear- or plastid-encoded polypeptides revealed that uncoupled LHC may be responsible for the high wavelength-fluorescence contribution observed around 700-710 nm. There is no evidence for the synthesis of new chlorophyll-protein complexes.
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Affiliation(s)
- Thibaut E Desquilbet
- Organismes Photosynthétiques et Environnement, CNRS-ENS FRE2433, Département de Biologie de l'Ecole Normale Supérieure, 46 rue d'Ulm, F-75230 Paris Cedex 05, France
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Colas C, Ortiz de Montellano PR. Autocatalytic radical reactions in physiological prosthetic heme modification. Chem Rev 2003; 103:2305-32. [PMID: 12797831 DOI: 10.1021/cr0204303] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Christophe Colas
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143-0446, USA
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Auclair K, Huang HW, Moënne-Loccoz P, Ortiz de Montellano PR. Cloning and expression of a heme binding protein from the genome of Saccharomyces cerevisiae. Protein Expr Purif 2003; 28:340-9. [PMID: 12699699 DOI: 10.1016/s1046-5928(02)00699-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The YLR205c gene of Saccharomyces cerevisiae does not show significant sequence identity to any known gene, except for heme oxygenase (22% to human HO-1). The YLR205 ORF was cloned and overexpressed in both Escherichia coli and S. cerevisiae. Both expression systems yielded proteins that bound heme tightly. The isolated YLR205c protein underwent reduction in the presence of either NADPH-cytochrome P450 reductase or NADH-putidaredoxin-putidaredoxin reductase but did not exhibit heme oxygenase activity. The protein exhibited modest H(2)O(2)-dependent peroxidase activities with guaiacol, potassium iodide, and 2,2(')-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS). Thus, YLR205c codes for a hemoprotein of unknown physiological function that exhibits peroxidase activity.
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Affiliation(s)
- Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 2K6.
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Muramoto T, Tsurui N, Terry MJ, Yokota A, Kohchi T. Expression and biochemical properties of a ferredoxin-dependent heme oxygenase required for phytochrome chromophore synthesis. PLANT PHYSIOLOGY 2002; 130:1958-66. [PMID: 12481078 PMCID: PMC166706 DOI: 10.1104/pp.008128] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2002] [Revised: 06/18/2002] [Accepted: 08/29/2002] [Indexed: 05/19/2023]
Abstract
The HY1 gene of Arabidopsis encodes a plastid heme oxygenase (AtHO1) required for the synthesis of the chromophore of the phytochrome family of plant photoreceptors. To determine the enzymatic properties of plant heme oxygenases, we have expressed the HY1 gene (without the plastid transit peptide) in Escherichia coli to produce an amino terminal fusion protein between AtHO1 and glutathione S-transferase. The fusion protein was soluble and expressed at high levels. Purified recombinant AtHO1, after glutathione S-transferase cleavage, is a hemoprotein that forms a 1:1 complex with heme. In the presence of reduced ferredoxin, AtHO1 catalyzed the formation of biliverdin IXalpha from heme with the concomitant production of carbon monoxide. Heme oxygenase activity could also be reconstituted using photoreduced ferredoxin generated through light irradiation of isolated thylakoid membranes, suggesting that ferredoxin may be the electron donor in vivo. In addition, AtHO1 required an iron chelator and second reductant, such as ascorbate, for full activity. These results show that the basic mechanism of heme cleavage has been conserved between plants and other organisms even though the function, subcellular localization, and cofactor requirements of heme oxygenases differ substantially.
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Affiliation(s)
- Takuya Muramoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
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Simpson CL, Stern DB. The treasure trove of algal chloroplast genomes. Surprises in architecture and gene content, and their functional implications. PLANT PHYSIOLOGY 2002; 129:957-66. [PMID: 12114552 PMCID: PMC1540241 DOI: 10.1104/pp.010908] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Clare L Simpson
- Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, Ithaca, New York 14853, USA
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Abstract
Group II introns have attracted considerable attention as ribozymes, mobile genetic elements and possible progenitors of nuclear spliceosomal introns. Major advances in understanding their catalytic structure and dispersal strategies have recently come from several model mitochondrial and bacterial self-splicing introns. In Nature, this family of introns shows wide variation in both features and behaviour, and this review includes a focus on the diversity of evolutionary pathways taken.
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Affiliation(s)
- L Bonen
- Biology Dept, University of Ottawa, 30 Marie Curie St, Ottawa, Canada K1N 6N5.
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Davis SJ, Bhoo SH, Durski AM, Walker JM, Vierstra RD. The heme-oxygenase family required for phytochrome chromophore biosynthesis is necessary for proper photomorphogenesis in higher plants. PLANT PHYSIOLOGY 2001; 126:656-69. [PMID: 11402195 PMCID: PMC111157 DOI: 10.1104/pp.126.2.656] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The committed step in the biosynthesis of the phytochrome chromophore phytochromobilin involves the oxidative cleavage of heme by a heme oxygenase (HO) to form biliverdin IXalpha. Through positional cloning of the photomorphogenic mutant hy1, the Arabidopsis HO (designated AtHO1) responsible for much of phytochromobilin synthesis recently was identified. Using the AtHO1 sequence, we identified families of HO genes in a number of plants that cluster into two subfamilies (HO1- and HO2-like). The tomato (Lycopersicon esculentum) yg-2 and Nicotiana plumbaginifolia pew1 photomorphogenic mutants are defective in specific HO genes. Phenotypic analysis of a T-DNA insertion mutant of Arabidopsis HO2 revealed that the second HO subfamily also contributes to phytochromobilin synthesis. Homozygous ho2-1 plants show decreased chlorophyll accumulation, reduced growth rate, accelerated flowering time, and reduced de-etiolation. A mixture of apo- and holo-phyA was detected in etiolated ho2-1 seedlings, suggesting that phytochromobilin is limiting in this mutant, even in the presence of functional AtHO1. The patterns of Arabidopsis HO1 and HO2 expression suggest that the products of both genes overlap temporally and spatially. Taken together, the family of HOs is important for phytochrome-mediated development in a number of plants and that each family member may uniquely contribute to the phytochromobilin pool needed to assemble holo-phytochromes.
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Affiliation(s)
- S J Davis
- Laboratory of Genetics, Cellular and Molecular Biology Program, and the Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706, USA
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Richaud C, Zabulon G, Joder A, Thomas JC. Nitrogen or sulfur starvation differentially affects phycobilisome degradation and expression of the nblA gene in Synechocystis strain PCC 6803. J Bacteriol 2001; 183:2989-94. [PMID: 11325925 PMCID: PMC95197 DOI: 10.1128/jb.183.10.2989-2994.2001] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrogen (N) limitation in cyanobacteria is well documented: a reduced growth rate is observed, accompanied by a cessation of phycobiliprotein synthesis and an ordered degradation of phycobilisomes (PBS). This leads to a dramatic bleaching phenomenon known as chlorosis. In Synechococcus strain PCC 7942, bleaching due to PBS degradation is also observed under sulfur (S) or phosphorus (P) limitation, and all three are under the control of the nblA gene product, a 59-amino-acid polypeptide which is overexpressed under N, S, and P starvation (J. L. Collier, and A. R. Grossman, EMBO J. 13:1039-1047, 1994). Cyanobase sequence data for Synechocystis strain PCC 6803 indicate the presence of two tandem open reading frames (sll0452 and sll0453) homologous to nblA. We cloned the two genes, identified a unique 5' mRNA end suggestive of a single transcription start site, and studied nblA expression under conditions of N or S starvation by Northern hybridization: transcripts were detected only under N starvation (no signal is detected in replete medium or with S starvation), whether nblA1 or nblA2 was used as a probe. Mutations in nblA1 and nblA2 were constructed by insertion of a kanamycin cassette; both mutations were nonbleaching under N starvation. Synechocystis strain PCC 6803 does not bleach under S starvation, consistent with the absence of nblA induction in these conditions. These results were confirmed by analysis of the PBS components: sequential degradation of phycocyanin and associated linkers was observed only under conditions of N starvation. This indicates differences between Synechocystis strain PCC 6803 and Synechococcus strain PCC 7942 in their regulatory and signaling pathways leading to N- and S-starved phenotypes.
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Affiliation(s)
- C Richaud
- Unité Mixte de Recherche 8543, Centre National de la Recherche Scientifique, "Photorégulation et Dynamique des Membranes Végétales," Ecole Normale Supérieure, 75230 Paris cedex 05, France.
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Frankenberg N, Mukougawa K, Kohchi T, Lagarias JC. Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms. THE PLANT CELL 2001; 13:965-78. [PMID: 11283349 PMCID: PMC135530 DOI: 10.1105/tpc.13.4.965] [Citation(s) in RCA: 147] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2000] [Accepted: 01/27/2001] [Indexed: 05/21/2023]
Abstract
Phytobilins are linear tetrapyrrole precursors of the light-harvesting prosthetic groups of the phytochrome photoreceptors of plants and the phycobiliprotein photosynthetic antennae of cyanobacteria, red algae, and cryptomonads. Previous biochemical studies have established that phytobilins are synthesized from heme via the intermediacy of biliverdin IX alpha (BV), which is reduced subsequently by ferredoxin-dependent bilin reductases with different double-bond specificities. By exploiting the sequence of phytochromobilin synthase (HY2) of Arabidopsis, an enzyme that catalyzes the ferredoxin-dependent conversion of BV to the phytochrome chromophore precursor phytochromobilin, genes encoding putative bilin reductases were identified in the genomes of various cyanobacteria, oxyphotobacteria, and plants. Phylogenetic analyses resolved four classes of HY2-related genes, one of which encodes red chlorophyll catabolite reductases, which are bilin reductases involved in chlorophyll catabolism in plants. To test the catalytic activities of these putative enzymes, representative HY2-related genes from each class were amplified by the polymerase chain reaction and expressed in Escherichia coli. Using a coupled apophytochrome assembly assay and HPLC analysis, we examined the ability of the recombinant proteins to catalyze the ferredoxin-dependent reduction of BV to phytobilins. These investigations defined three new classes of bilin reductases with distinct substrate/product specificities that are involved in the biosynthesis of the phycobiliprotein chromophore precursors phycoerythrobilin and phycocyanobilin. Implications of these results are discussed with regard to the pathways of phytobilin biosynthesis and their evolution.
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Affiliation(s)
- N Frankenberg
- Section of Molecular and Cellular Biology, University of California at Davis, One Shields Avenue, Davis, California 95616, USA
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Foury F, Talibi D. Mitochondrial control of iron homeostasis. A genome wide analysis of gene expression in a yeast frataxin-deficient strain. J Biol Chem 2001; 276:7762-8. [PMID: 11112771 DOI: 10.1074/jbc.m005804200] [Citation(s) in RCA: 146] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deletion of YFH1, the yeast frataxin homologue gene, elicits mitochondrial iron accumulation and alters cellular iron homeostasis. Here, we report a genome wide analysis of gene expression in a yfh1(DeltaYFH1) deleted strain. Frataxin deficiency results in enhanced expression of some 70 genes including a set of genes, called the iron regulon, that are under the control of the iron-sensing transcription factor AFT1. Five new AFT1-dependent genes, YOR382w, YOR383c, YDR534c, YLR136c, and YLR205c were found. The first three genes presumably encode cell-wall glycosylphosphatidylinositol anchor proteins and exhibit a 30-100-fold increased expression. The triple deletion of these genes decreases efficiency in utilization of the iron of ferrioxamine B by the yeast cell. YLR136c bears homology to tristetraproline proteins, which are post-transcriptional regulators in mammalian cells. Deletion of YLR136c increases the mRNA levels of iron regulon members. YLR205c bears homology to heme oxygenases. Our data show that frataxin deficiency elicits iron mobilization from all iron sources in an AFT1-dependent manner. Wild-type and DeltaYFH1 glycerol-grown cells exhibit similar high respiration rates, no mitochondrial iron accumulation, and high expression of the iron regulon, suggesting that under these conditions little iron is extruded from mitochondria. These data suggest that the activity of Yfh1p is not essential in cells grown on glycerol. This study has also revealed unexpected links between mitochondria and remote metabolic pathways since frataxin deficiency also enhances the expression of genes such as HSP30, that escape to AFT1 control. Finally, no oxidative stress gene is induced.
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Affiliation(s)
- F Foury
- Unité de Biochimie Physiologique, Place Croix du Sud, 2-20, 1348 Louvain-la-Neuve, Belgium.
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Hess WR, Rocap G, Ting CS, Larimer F, Stilwagen S, Lamerdin J, Chisholm SW. The photosynthetic apparatus of Prochlorococcus: Insights through comparative genomics. PHOTOSYNTHESIS RESEARCH 2001; 70:53-71. [PMID: 16228362 DOI: 10.1023/a:1013835924610] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Within the vast oceanic gyres, a significant fraction of the total chlorophyll belongs to the light-harvesting antenna systems of a single genus, Prochlorococcus. This organism, discovered only about 10 years ago, is an extremely small, Chl b-containing cyanobacterium that sometimes constitutes up to 50% of the photosynthetic biomass in the oceans. Various Prochlorococcus strains are known to have significantly different conditions for optimal growth and survival. Strains which dominate the surface waters, for example, have an irradiance optimum for photosynthesis of 200 mumol photons m(-2) s(-1), whereas those that dominate the deeper waters photosynthesize optimally at 30-50 mumol photons m(-2) s(-1). These high and low light adapted 'ecotypes' are very closely related - less than 3% divergent in their 16S rRNA sequences - inviting speculation as to what features of their photosynthetic mechanisms might account for the differences in photosynthetic performance. Here, we compare information obtained from the complete genome sequences of two Prochlorococcus strains, with special emphasis on genes for the photosynthetic apparatus. These two strains, Prochlorococcus MED4 and MIT 9313, are representatives of high- and low-light adapted ecotypes, characterized by their low or high Chl b/a ratio, respectively. Both genomes appear to be significantly smaller (1700 and 2400 kbp) than those of other cyanobacteria, and the low-light-adapted strain has significantly more genes than its high light counterpart. In keeping with their comparative light-dependent physiologies, MED4 has many more genes encoding putative high-light-inducible proteins (HLIP) and photolyases to repair UV-induced DNA damage, whereas MIT 9313 possesses more genes associated with the photosynthetic apparatus. These include two pcb genes encoding Chl-binding proteins and a second copy of the gene psbA, encoding the Photosystem II reaction center protein D1. In addition, MIT 9313 contains a gene cluster to produce chromophorylated phycoerythrin. The latter represents an intermediate form between the phycobiliproteins of non-Chl b containing cyanobacteria and an extremely modified beta phycoerythrin as the sole derivative of phycobiliproteins still present in MED4. Intriguing features found in both Prochlorococcus strains include a gene cluster for Rubisco and carboxysomal proteins that is likely of non-cyanobacterial origin and two genes for a putative varepsilon and beta lycopene cyclase, respectively, explaining how Prochlorococcus may synthesize the alpha branch of carotenoids that are common in green organisms but not in other cyanobacteria.
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Affiliation(s)
- W R Hess
- Humboldt-University, Berlin, Germany
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Giraud E, Hannibal L, Fardoux J, Verméglio A, Dreyfus B. Effect of Bradyrhizobium photosynthesis on stem nodulation of Aeschynomene sensitiva. Proc Natl Acad Sci U S A 2000; 97:14795-800. [PMID: 11114184 PMCID: PMC18998 DOI: 10.1073/pnas.250484097] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Some leguminous species of the genus Aeschynomene are specifically stem-nodulated by photosynthetic bradyrhizobia. To study the effect of bacterial photosynthesis during symbiosis, we generated a photosynthesis-negative mutant of the Bradyrhizobium sp. strain ORS278 symbiont of Aeschynomene sensitiva. The presence of a functional photosynthetic unit in bacteroids and the high expression of the photosynthetic genes observed in stem nodules demonstrate that the bacteria are photosynthetically active during stem symbiosis. Stem inoculation by the photosynthetic mutant gave a 50% decrease in stem-nodule number, which reduced nitrogen fixation activity and plant growth in the same proportion. These results indicate an important role of bacterial photosynthesis in the efficiency of stem nodulation.
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Affiliation(s)
- E Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut de Recherche pour le Développement, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Ecole Nationale d'Agronomie de Montpellier, Cedex, France
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Ritz M, Thomas JC, Spilar A, Etienne AL. Kinetics of photoacclimation in response to a shift to high light of the red alga Rhodella violacea adapted to low irradiance. PLANT PHYSIOLOGY 2000; 123:1415-26. [PMID: 10938358 PMCID: PMC59098 DOI: 10.1104/pp.123.4.1415] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/1999] [Accepted: 04/03/2000] [Indexed: 05/21/2023]
Abstract
The unicellular rhodophyte Rhodella violacea can adapt to a wide range of irradiances. To create a light stress, cells acclimated to low light were transferred to higher irradiance and the kinetics of various changes produced by the light shift were analyzed. The proton gradient generated by excess light led to a non-photochemical quenching of the chlorophyll fluorescence and some photoinhibition of photosystem II centers was also produced by the light stress. After the shift to higher irradiance, the mRNA levels of three chloroplast genes that encode phycoerythrin and phycocyanin apoproteins and heme oxygenase (the first enzyme specific to the bilin synthesis) were negatively regulated. A change in the amount of thylakoids and in the total pigment content of the cells occurred during light acclimation after a light stress. The change in the size of the phycobilisome was limited to dissapearance of the terminal phycoerythrin hexamers in some of the rods. The ability of R. violacea to photoacclimate depends both on large changes in thylakoid number and pigment content and on smaller changes in the antenna size of photosystem II.
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Affiliation(s)
- M Ritz
- Laboratoire Dynamique des Membranes Végétales-Complexes Proteines-Pigments, Unité de Recherche Associée 1810 Centre National de la Recherche Scientifique, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris cedex 05, France
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Zhu W, Hunt DJ, Richardson AR, Stojiljkovic I. Use of heme compounds as iron sources by pathogenic neisseriae requires the product of the hemO gene. J Bacteriol 2000; 182:439-47. [PMID: 10629191 PMCID: PMC94294 DOI: 10.1128/jb.182.2.439-447.2000] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Heme compounds are an important source of iron for neisseriae. We have identified a neisserial gene, hemO, that is essential for heme, hemoglobin (Hb), and haptoglobin-Hb utilization. The hemO gene is located 178 bp upstream of the hmbR Hb receptor gene in Neisseria meningitidis isolates. The product of the hemO gene is homologous to enzymes that degrade heme; 21% of its amino acid residues are identical, and 44% are similar, to those of the human heme oxygenase-1. DNA sequences homologous to hemO were ubiquitous in commensal and pathogenic neisseriae. HemO genetic knockout strains of Neisseria gonorrhoeae and N. meningitidis were unable to use any heme source, while the assimilation of transferrin-iron and iron-citrate complexes was unaffected. A phenotypic characterization of a conditional hemO mutant, constructed by inserting an isopropyl-beta-D-thiogalactopyranoside (IPTG)-regulated promoter upstream of the ribosomal binding site of hemO, confirmed the indispensability of the HemO protein in heme utilization. The expression of HemO also protected N. meningitidis cells against heme toxicity. hemO mutants were still able to transport heme into the cell, since both heme and Hb could complement an N. meningitidis hemA hemO double mutant for growth. The expression of the HmbR receptor was reduced significantly by the inactivation of the hemO gene, suggesting that hemO and hmbR are transcriptionally linked. The expression of the unlinked Hb receptor, HpuAB, was not altered. Comparison of the polypeptide patterns of the wild type and the hemO mutant led to detection of six protein spots with an altered expression pattern, suggesting a more general role of HemO in the regulation of gene expression in Neisseriae.
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Affiliation(s)
- W Zhu
- Department of Microbiology, Emory School of Medicine, Atlanta, Georgia 30322, USA
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Thomas JC, Passaquet C. Characterization of a phycoerythrin without alpha-subunits from a unicellular red alga. J Biol Chem 1999; 274:2472-82. [PMID: 9891018 DOI: 10.1074/jbc.274.4.2472] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We describe here the spectral and biochemical properties of a novel biliprotein belonging to the phycoerythrin family, purified from the phycobilisome of a unicellular red alga, Rhodella reticulata strain R6. This biliprotein is assembled from a unique beta-type subunit, chloroplast-encoded, whose hexameric or dodecameric aggregates are stabilized by unusually large linkers (87 and 60 kDa) encoded by the nuclear genome. Although each beta-type subunit bears two phycoerythrobilins and one phycocyanobilin per chain, the linker polypeptides are non-chromophorylated. The apoprotein of the beta-subunit of the R. reticulata R6 phycoerythrin is specified by a monocistronic rpeB chloroplast gene that is split into three exons. We discuss the relationships between R6 beta-phycoerythrin and the previously published polypeptide sequences, the structural consequences due to the absence of an alpha-subunit, and its evolutionary implications.
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Affiliation(s)
- J C Thomas
- Laboratoire de Photorégulation et Dynamique des Membranes Végétales, CNRS, Unité de Recherche Associée 1810, GDR 1002, Ecole Normale Supérieure, 46 rue d'Ulm, 75 230 Paris Cedex 05, France.
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Cornejo J, Willows RD, Beale SI. Phytobilin biosynthesis: cloning and expression of a gene encoding soluble ferredoxin-dependent heme oxygenase from Synechocystis sp. PCC 6803. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 15:99-107. [PMID: 9744099 DOI: 10.1046/j.1365-313x.1998.00186.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The phytobilin chromophores of phycobiliproteins and phytochromes are biosynthesized from heme in a pathway that begins with the opening of the tetrapyrrole macrocycle of protoheme to form biliverdin IX alpha, in a reaction catalyzed by heme oxygenase. A gene containing an open reading frame with a predicted polypeptide that has a sequence similar to that of a conserved region of animal microsomal heme oxygenases was identified in the published genomic sequence of Synechocystis sp. PCC 6803. This gene, named ho1, was cloned and expressed in Escherichia coli under the control of the lacZ promoter. Cells expressing the gene became green colored due to the accumulation of biliverdin IX alpha. The size of the expressed protein was equal to the predicted size of the Synechocystis gene product, named HO1. Heme oxygenase activity was assayed in incubations containing extract of transformed E. coli cells. Incubations containing extract of induced cells, but not those containing extract of uninduced cells, had ferredoxin-dependent heme oxygenase activity. With mesoheme as the substrate, the reaction product was identified as mesobiliverdin IX alpha by spectrophotometry and reverse-phase HPLC. Heme oxygenase activity was not sedimented by centrifugation at 100, 000 g. Expression of HO1 increased several-fold during incubation of the cells for 72 h in iron-deficient medium.
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Affiliation(s)
- J Cornejo
- Division of Biology and Medicine, Brown University, Providence, Rhode Island 02912, USA
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