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Kohata R, Lim H, Kanamoto Y, Murakami A, Fujita Y, Tanaka A, Swingley W, Ito H, Tanaka R. Heterologous complementation systems verify the mosaic distribution of three distinct protoporphyrinogen IX oxidase in the cyanobacterial phylum. J Plant Res 2023; 136:107-115. [PMID: 36357749 DOI: 10.1007/s10265-022-01423-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
The pathways for synthesizing tetrapyrroles, including heme and chlorophyll, are well-conserved among organisms, despite the divergence of several enzymes in these pathways. Protoporphyrinogen IX oxidase (PPOX), which catalyzes the last common step of the heme and chlorophyll biosynthesis pathways, is encoded by three phylogenetically-unrelated genes, hemY, hemG and hemJ. All three types of homologues are present in the cyanobacterial phylum, showing a mosaic phylogenetic distribution. Moreover, a few cyanobacteria appear to contain two types of PPOX homologues. Among the three types of cyanobacterial PPOX homologues, only a hemJ homologue has been experimentally verified for its functionality. An objective of this study is to provide experimental evidence for the functionality of the cyanobacterial PPOX homologues by using two heterologous complementation systems. First, we introduced hemY and hemJ homologues from Gloeobacter violaceus PCC7421, hemY homologue from Trichodesmium erythraeum, and hemG homologue from Prochlorococcus marinus MIT9515 into a ΔhemG strain of E. coli. hemY homologues from G. violaceus and T. erythraeum, and the hemG homologue of P. marinus complimented the E. coli strain. Subsequently, we attempted to replace the endogenous hemJ gene of the cyanobacterium Synechocystis sp. PCC6803 with the four PPOX homologues mentioned above. Except for hemG from P. marinus, the other PPOX homologues substituted the function of hemJ in Synechocystis. These results show that all four homologues encode functional PPOX. The transformation of Synechocystis with G. violaceus hemY homologue rendered the cells sensitive to an inhibitor of the HemY-type PPOX, acifluorfen, indicating that the hemY homologue is sensitive to this inhibitor, while the wild-type G. violaceus was tolerant to it, most likely due to the presence of HemJ protein. These results provide an additional level of evidence that G. violaceus contains two types of functional PPOX.
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Affiliation(s)
- Ryoya Kohata
- Institute of Low Temperature Science, Hokkaido University, N19W8, Kita-Ku, Sapporo, 060-0819, Japan
| | - HyunSeok Lim
- Institute of Low Temperature Science, Hokkaido University, N19W8, Kita-Ku, Sapporo, 060-0819, Japan
| | - Yuki Kanamoto
- Research Center of Inland Seas, Kobe University, Awaji, 656-2401, Japan
| | - Akio Murakami
- Research Center of Inland Seas, Kobe University, Awaji, 656-2401, Japan
- Department of Biology, Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19W8, Kita-Ku, Sapporo, 060-0819, Japan
| | - Wesley Swingley
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Hisashi Ito
- Institute of Low Temperature Science, Hokkaido University, N19W8, Kita-Ku, Sapporo, 060-0819, Japan
| | - Ryouichi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19W8, Kita-Ku, Sapporo, 060-0819, Japan.
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Deery E, Lawrence AD, Warren MJ. Biosynthesis of cobamides: Methods for the detection, analysis and production of cobamides and biosynthetic intermediates. Methods Enzymol 2022; 668:3-23. [PMID: 35589198 DOI: 10.1016/bs.mie.2022.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vitamin B12, cobalamin, belongs to the broader cobamide family whose members are characterized by the presence of a cobalt-containing corrinoid ring. The ability to detect, isolate and characterize cobamides and their biosynthetic intermediates is an important prerequisite when attempting to study the synthesis of this remarkable group of compounds that play diverse roles across the three kingdoms of life. The synthesis of cobamides is restricted to only certain prokaryotes and their structural complexity entails an equally complex synthesis orchestrated through a multi-step biochemical pathway. In this chapter, we have outlined methods that we have found extremely helpful in the characterization of the biochemical pathway, including a plate microbiological assay, a corrinoid affinity extraction method, LCMS characterization and a multigene cloning strategy.
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Ceriotti LF, Roulet ME, Sanchez-Puerta MV. Plastomes in the holoparasitic family Balanophoraceae: Extremely high AT content, severe gene content reduction, and two independent genetic code changes. Mol Phylogenet Evol 2021; 162:107208. [PMID: 34029719 DOI: 10.1016/j.ympev.2021.107208] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 05/11/2021] [Accepted: 05/19/2021] [Indexed: 12/29/2022]
Abstract
The transition to a heterotrophic lifestyle in angiosperms is characterized by convergent evolutionary changes. Plastid genome remodeling includes dramatic functional and physical reductions with the highest degrees observed in fully heterotrophic plants. Genes related to photosynthesis are generally absent or pseudogenized, while a few genes related to other metabolic processes that take place within the plastid are almost invariably maintained. The family Balanophoraceae consists of root holoparasites that present reduced plastid genomes with an extraordinarily elevated AT content and the single genetic code change ever documented in land plant plastomes (the stop codon TAG now codes for tryptophan). Here, we studied the plastomes of Lophophytum leandri and Ombrophytum subterraneum (Balanophoraceae) that showed the remarkable absence of the gene trnE, a highly biased nucleotide composition, and an independent genetic code change (the standard stop codon TGA codes for tryptophan). This is the second genetic code change identified in land plant plastomes. Analysis of the transcriptome of Lophophytum indicated that the entire C5 pathway typical of plants is conserved despite the lack of trnE in its plastome. A hypothetical model of plastome evolution in the Balanophoraceae is presented.
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Affiliation(s)
- Luis Federico Ceriotti
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB Chacras de Coria, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina
| | - M Emilia Roulet
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB Chacras de Coria, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB Chacras de Coria, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina.
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Chambers IG, Willoughby MM, Hamza I, Reddi AR. One ring to bring them all and in the darkness bind them: The trafficking of heme without deliverers. Biochim Biophys Acta Mol Cell Res 2021; 1868:118881. [PMID: 33022276 PMCID: PMC7756907 DOI: 10.1016/j.bbamcr.2020.118881] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023]
Abstract
Heme, as a hydrophobic iron-containing organic ring, is lipid soluble and can interact with biological membranes. The very same properties of heme that nature exploits to support life also renders heme potentially cytotoxic. In order to utilize heme, while also mitigating its toxicity, cells are challenged to tightly control the concentration and bioavailability of heme. On the bright side, it is reasonable to envision that, analogous to other transition metals, a combination of membrane-bound transporters, soluble carriers, and chaperones coordinate heme trafficking to subcellular compartments. However, given the dual properties exhibited by heme as a transition metal and lipid, it is compelling to consider the dark side: the potential role of non-proteinaceous biomolecules including lipids and nucleic acids that bind, sequester, and control heme trafficking and bioavailability. The emergence of inter-organellar membrane contact sites, as well as intracellular vesicles derived from various organelles, have raised the prospect that heme can be trafficked through hydrophobic channels. In this review, we aim to focus on heme delivery without deliverers - an alternate paradigm for the regulation of heme homeostasis through chaperone-less pathways for heme trafficking.
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Affiliation(s)
- Ian G Chambers
- Department of Animal and Avian Sciences, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20740, United States of America
| | - Mathilda M Willoughby
- School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, United States of America
| | - Iqbal Hamza
- Department of Animal and Avian Sciences, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20740, United States of America.
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, United States of America.
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Fushimi K, Narikawa R. Phytochromes and Cyanobacteriochromes: Photoreceptor Molecules Incorporating a Linear Tetrapyrrole Chromophore. Adv Exp Med Biol 2021; 1293:167-87. [PMID: 33398813 DOI: 10.1007/978-981-15-8763-4_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this chapter, we summarize the molecular mechanisms of the linear tetrapyrrole-binding photoreceptors, phytochromes, and cyanobacteriochromes. We especially focus on the color-tuning mechanisms and conformational changes during the photoconversion process. Furthermore, we introduce current status of development of the optogenetic tools based on these molecules. Huge repertoire of these photoreceptors with diverse spectral properties would contribute to development of multiplex optogenetic regulation. Among them, the photoreceptors incorporating the biliverdin IXα chromophore is advantageous for in vivo optogenetics because this is intrinsic in the mammalian cells, and absorbs far-red light penetrating into deep mammalian tissues.
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Layer G. Heme biosynthesis in prokaryotes. Biochim Biophys Acta Mol Cell Res 2020; 1868:118861. [PMID: 32976912 DOI: 10.1016/j.bbamcr.2020.118861] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022]
Abstract
The cyclic tetrapyrrole heme is used as a prosthetic group in a broad variety of different proteins in almost all organisms. Often, it is essential for vital biochemical processes such as aerobic and anaerobic respiration as well as photosynthesis. In Nature, heme is made from the common tetrapyrrole precursor 5-aminolevulinic acid, and for a long time it was assumed that heme is biosynthesized by a single, common pathway in all organisms. However, although this is indeed the case in eukaryotes, heme biosynthesis is more diverse in the prokaryotic world, where two additional pathways exist. The final elucidation of the two 'alternative' heme biosynthesis routes operating in some bacteria and archaea was achieved within the last decade. This review summarizes the three different heme biosynthesis pathways with a special emphasis on the two 'new' prokaryotic routes.
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Affiliation(s)
- Gunhild Layer
- Albert-Ludwigs-Universität Freiburg, Institut für Pharmazeutische Wissenschaften, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany.
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Adir N, Bar-Zvi S, Harris D. The amazing phycobilisome. Biochim Biophys Acta Bioenerg 2019; 1861:148047. [PMID: 31306623 DOI: 10.1016/j.bbabio.2019.07.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/19/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Cyanobacteria and red-algae share a common light-harvesting complex which is different than all other complexes that serve as photosynthetic antennas - the Phycobilisome (PBS). The PBS is found attached to the stromal side of thylakoid membranes, filling up most of the gap between individual thylakoids. The PBS self assembles from similar homologous protein units that are soluble and contain conserved cysteine residues that covalently bind the light absorbing chromophores, linear tetra-pyrroles. Using similar construction principles, the PBS can be as large as 16.8 MDa (68×45×39nm), as small as 1.2 MDa (24 × 11.5 × 11.5 nm), and in some unique cases smaller still. The PBS can absorb light between 450 nm to 650 nm and in some cases beyond 700 nm, depending on the species, its composition and assembly. In this review, we will present new observations and structures that expand our understanding of the distinctive properties that make the PBS an amazing light harvesting system. At the end we will suggest why the PBS, for all of its excellent properties, was discarded by photosynthetic organisms that arose later in evolution such as green algae and higher plants.
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Affiliation(s)
- Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel.
| | - Shira Bar-Zvi
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Dvir Harris
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
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Yadav O, Varshney A, Kumar A, Ratnesh RK, Mehata MS. A 2B corroles: Fluorescence signaling systems for sensing fluoride ions. Spectrochim Acta A Mol Biomol Spectrosc 2018; 202:207-213. [PMID: 29787917 DOI: 10.1016/j.saa.2018.05.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 05/10/2018] [Accepted: 05/14/2018] [Indexed: 06/08/2023]
Abstract
Four free base corroles, 1-4, A2B, (where A = nitrophenyl, and B = pentafluorophenyl, 2, 6-difluoro, 3, 4, 5-trifluoro and 4-carboxymethylphenyl group) have been synthesized, characterized and demonstrated as excellent chemosensor for the detection of fluoride ions selectively in toluene solution. The reported corroles shows highest quantum yield in free base form of porphyrinoid systems so far. All these corrole, 1-4, have the excellent ability to sense fluoride ion. Cumulative effect of static and dynamic factors is responsible for the quenching of fluorescence which indicates the detection of fluoride ion in solution.
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Affiliation(s)
- Omprakash Yadav
- Department of Applied Chemistry, Delhi Technological University, Delhi 42, India
| | - Atul Varshney
- Department of Applied Chemistry, Delhi Technological University, Delhi 42, India
| | - Anil Kumar
- Department of Applied Chemistry, Delhi Technological University, Delhi 42, India.
| | | | - Mohan Singh Mehata
- Department of Applied Physics, Delhi Technological University, Delhi 42, India
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Zhao A, Han F. Crystal structure of Arabidopsis thaliana glutamyl-tRNA Glu reductase in complex with NADPH and glutamyl-tRNA Glu reductase binding protein. Photosynth Res 2018; 137:443-452. [PMID: 29785497 DOI: 10.1007/s11120-018-0518-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
In higher plants, the tetrapyrrole biosynthesis pathway starts from the reaction catalyzed by the rate-limiting enzyme, glutamyl-tRNAGlu reductase (GTR). In Arabidopsis thaliana, GTR is controlled by post-transcriptional regulators such as GTR binding protein (GBP), which stimulates AtGTR activity. The NADPH-binding domain of AtGTR undergoes a substantial movement upon GBP binding. Here, we report the crystal structure of AtGTR-NADPH-GBP ternary complex. NADPH binding causes slight structural changes compared with the AtGTR-GBP binary complex, and possibly take a part of the space needed by the substrate glutamyl-tRNAGlu. The highly reactive sulfhydryl group of the active-site residue Cys144 shows an obvious rotation, which may facilitate the hydride transfer from NADPH to the thioester intermediate to form glutamate-1-semialdehyde. Furthermore, Lys271, Lys274, Ser275, Asn278, and Gln282 of GBP participate in the interaction between AtGTR and GBP, and the stimulating effect of GBP decreased when all of these residues were mutated to Ala. When the Cys144 of AtGTR was mutated to Ser, AtGTR activity could not be detected even in the presence of GBP.
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Affiliation(s)
- Aiguo Zhao
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Feng Han
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Zeng X, Bai L, Wei Z, Yuan H, Wang Y, Xu Q, Tang Y, Nyima T. Transcriptome analysis revealed the drought-responsive genes in Tibetan hulless barley. BMC Genomics 2016; 17:386. [PMID: 27207260 PMCID: PMC4875595 DOI: 10.1186/s12864-016-2685-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/22/2016] [Indexed: 12/05/2022] Open
Abstract
Background Hulless barley, also called naked barley, is an important cereal crop worldwide, serving as a healthy food both for human consumption and animal feed. Nevertheless, it often suffered from drought stress during its growth and development, resulting in a drastic reduction in barley yields. Therefore, study on molecular mechanism of hulless barley drought-tolerance is very important for increasing barley production. To investigate molecular mechanism of barley drought-resistance, this study examined co-regulated mRNAs that show a change in expression pattern under early well water, later water deficit and finally water recovery treatments, and to identify mRNAs specific to water limiting conditions. Results Total of 853 differentially expressed genes (DEGs) were detected and categorized into nine clusters, in which VI and VIII were apparently up-regulated under low relative soil moisture content (RSMC) level. The majority of genes in these two clusters was relevant to abiotic stress responses in abscisic acid (ABA) dependent and independent signaling pathway, including NCED, PYR/PYL/RCAR, SnRK2, ABF, MYB/MYC, AP2/ERF family, LEA and DHN. In contrast, genes within clusters II and IV were generally down-regulated under water stress; cluster IX genes were up-regulated during water recovery response to both low and high RSMC levels. Genes in implicated in tetrapyrrole binding, photosystem and photosynthetic membrane were the most affected in cluster IX. Conclusion Taken together, our findings indicate that the responses of hulless barley to drought stress shows differences in the pathways and genes activated. Furthermore, all these genes displayed different sensitivities to soil water deficit and might be profitable for future drought tolerance improvement in barley and other crops. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2685-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xingquan Zeng
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Lijun Bai
- Chengdu Life Baseline Technology Co., LTD, Chengdu, 610041, China
| | - Zexiu Wei
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Hongjun Yuan
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China.,Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, 850002, China
| | - Yulin Wang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China.,Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, 850002, China
| | - Qijun Xu
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China.,Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, 850002, China
| | - Yawei Tang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China.,Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, 850002, China
| | - Tashi Nyima
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China. .,Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, 850002, China.
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Yu Q, Lim S, Rockwell NC, Martin SS, Clark Lagarias J, Ames JB. 1H, 15N, and 13C chemical shift assignments of cyanobacteriochrome NpR6012g4 in the red-absorbing dark state. Biomol NMR Assign 2016; 10:139-142. [PMID: 26482922 PMCID: PMC4789077 DOI: 10.1007/s12104-015-9653-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/16/2015] [Indexed: 06/05/2023]
Abstract
Cyanobacteriochrome (CBCR) photosensory proteins are phytochrome homologs using bilin chromophores for light sensing across the visible spectrum. NpR6012g4 is a CBCR from Nostoc punctiforme that serves as a model for a widespread CBCR subfamily with red/green photocycles. We report NMR chemical shift assignments for both the protein backbone and side-chain resonances of the red-absorbing dark state of NpR6012g4 (BMRB no. 26582).
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Affiliation(s)
- Qinhong Yu
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Sunghyuk Lim
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Nathan C Rockwell
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616, USA
| | - Shelley S Martin
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616, USA
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
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Naeher S, Lengger SK, Grice K. A new method for the rapid analysis of 1H-Pyrrole-2,5-diones (maleimides) in environmental samples by two-dimensional gas chromatography time-of-flight mass spectrometry. J Chromatogr A 2016; 1435:125-35. [PMID: 26850318 DOI: 10.1016/j.chroma.2016.01.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/11/2016] [Accepted: 01/11/2016] [Indexed: 11/17/2022]
Abstract
Maleimides (1H-Pyrrole-2,5-diones) are monopyrrolic pigment derivatives with specific alkyl side chains that can be directly linked to their tetrapyrrole precursors, most notably chlorophylls and bacteriochlorophylls. These compounds can be used as palaeoenvironmental indicators such as algal productivity and redox conditions in ancient and modern aquatic systems. Here, we present a new method using two-dimensional gas chromatography time-of-flight mass spectrometry (GC × GC-ToF-MS), which enables the rapid analysis of maleimides in complex mixtures and different matrices (e.g. sediments and soils), therefore largely simplifying the previous intricate maleimide purification protocol. This method also reduces the potential for bias associated with partial losses due to low recovery and the high volatility of maleimides. The maleimide distributions and concentrations obtained by GC × GC-ToF-MS were reproducible and in agreement with the previously used purification procedure followed by analysis with traditional gas chromatography-mass spectrometry (GC-MS). The new method also resolved previously unrecognised, partial coelution of some maleimides with unknown compounds by quantification with the m/z 75 fragment ion. Furthermore, the higher sensitivity enabled the detection of previously unrecognised and preliminarily identified maleimides based on their relative retention times. The new, easier, rapid and more sensitive GC×GC-ToF-MS method greatly facilitates the analysis of maleimides in environmental samples to study tetrapyrrole degradation processes and will further the development of maleimides as biomarkers for palaeoenvironmental reconstructions.
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Affiliation(s)
- Sebastian Naeher
- Curtin University, Western Australia Organic and Isotope Geochemistry Centre (WA-OIGC), Department of Chemistry, The Institute for Geoscience Research, GPO Box U1987, Perth, WA 6845, Australia.
| | - Sabine K Lengger
- Curtin University, Western Australia Organic and Isotope Geochemistry Centre (WA-OIGC), Department of Chemistry, The Institute for Geoscience Research, GPO Box U1987, Perth, WA 6845, Australia
| | - Kliti Grice
- Curtin University, Western Australia Organic and Isotope Geochemistry Centre (WA-OIGC), Department of Chemistry, The Institute for Geoscience Research, GPO Box U1987, Perth, WA 6845, Australia.
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Overkamp KE, Gasper R, Kock K, Herrmann C, Hofmann E, Frankenberg-Dinkel N. Insights into the biosynthesis and assembly of cryptophycean phycobiliproteins. J Biol Chem 2014; 289:26691-26707. [PMID: 25096577 DOI: 10.1074/jbc.m114.591131] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Phycobiliproteins are employed by cyanobacteria, red algae, glaucophytes, and cryptophytes for light-harvesting and consist of apoproteins covalently associated with open-chain tetrapyrrole chromophores. Although the majority of organisms assemble the individual phycobiliproteins into larger aggregates called phycobilisomes, members of the cryptophytes use a single type of phycobiliprotein that is localized in the thylakoid lumen. The cryptophyte Guillardia theta (Gt) uses phycoerythrin PE545 utilizing the uncommon chromophore 15,16-dihydrobiliverdin (DHBV) in addition to phycoerythrobilin (PEB). Both the biosynthesis and the attachment of chromophores to the apophycobiliprotein have not yet been investigated for cryptophytes. In this study, we identified and characterized enzymes involved in PEB biosynthesis. In addition, we present the first in-depth biochemical characterization of a eukaryotic phycobiliprotein lyase (GtCPES). Plastid-encoded HO (GtHo) was shown to convert heme into biliverdin IXα providing the substrate with a putative nucleus-encoded DHBV:ferredoxin oxidoreductase (GtPEBA). A PEB:ferredoxin oxidoreductase (GtPEBB) was found to convert DHBV to PEB, which is the substrate for the phycobiliprotein lyase GtCPES. The x-ray structure of GtCPES was solved at 2.0 Å revealing a 10-stranded β-barrel with a modified lipocalin fold. GtCPES is an S-type lyase specific for binding of phycobilins with reduced C15=C16 double bonds (DHBV and PEB). Site-directed mutagenesis identified residues Glu-136 and Arg-146 involved in phycobilin binding. Based on the crystal structure, a model for the interaction of GtCPES with the apophycobiliprotein CpeB is proposed and discussed.
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Affiliation(s)
- Kristina E Overkamp
- Physiology of Microorganisms, Faculty for Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Raphael Gasper
- Protein Crystallography, Faculty for Biology and Biotechnology, and Ruhr University Bochum, 44780 Bochum, Germany
| | - Klaus Kock
- Physical Chemistry I, Protein Interactions, Faculty for Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
| | - Christian Herrmann
- Physical Chemistry I, Protein Interactions, Faculty for Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty for Biology and Biotechnology, and Ruhr University Bochum, 44780 Bochum, Germany
| | - Nicole Frankenberg-Dinkel
- Physiology of Microorganisms, Faculty for Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany.
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Gledhill M. The detection of iron protoporphyrin (heme b) in phytoplankton and marine particulate material by electrospray ionisation mass spectrometry - comparison with diode array detection. Anal Chim Acta 2014; 841:33-43. [PMID: 25109859 DOI: 10.1016/j.aca.2014.06.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 06/20/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
Abstract
A mass spectrometric (MS) method for the identification of iron protoporphyrin (IX) (FePTP, heme b) in marine particulate material and phytoplankton is described. Electrospray ionisation of FePTP produced the molecular Fe(III)PTP(+) ion (m/z=616) or the pseudomolecular [Fe(II)PTP + H](+) ion (m/z=617), depending on the oxidation state of the central iron ion. Collision induced dissociation (CID) in the ion trap mass spectrometer resulted in a single detected product ion (m/z=557) indicative of loss of ethanoic acid from a carboxylic acid side chain. Widening the isolation width to 616±3 resulted in production of a mass spectrum demonstrating the distinctive isotopic ratio of the iron containing fragment, further increasing the specificity of the analysis. Selective reactant monitoring (SRM) of the fragment ion (m/z=557) was applied to the detection of FePTP after chromatography of ammoniacal OGP extracts of marine samples. The detection limit for FePTP analysed by SRM after chromatography was 1.2±0.5fmol. For phytoplankton samples, reasonably good agreement was achieved between results obtained with SRM and those obtained by monitoring absorbance at λ=400nm using a diode array detector (DAD). Use of SRM for analysis of particulate material obtained from the high latitude North Atlantic allowed for the analysis of FePTP in the presence of a co-eluting compound that interfered with detection by DAD. Simultaneous collection of mass spectra from m/z=300 to 1500 resulted in identification of the pseudomolecular ion for the interfering compound. The CID fragmentation pattern and UV-visible mass spectra indicated that the interfering compound was a previously unidentified chlorin type compound. Comparison of FePTP determined by SRM and DAD on samples where this compound could not be detected showed that results collected using the two methods correlated. The use of both MS and DAD results in a powerful tool for quantifying this important biogenic component of the particulate iron pool.
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Affiliation(s)
- Martha Gledhill
- Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton SO14 3ZH, UK.
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