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Nelson G, Strain A, Isu A, Rahnama A, Wakabayashi KI, Melvin AT, Kato N. Cells collectively migrate during ammonium chemotaxis in Chlamydomonas reinhardtii. Sci Rep 2023; 13:10781. [PMID: 37402785 DOI: 10.1038/s41598-023-36818-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 06/10/2023] [Indexed: 07/06/2023] Open
Abstract
The mechanisms governing chemotaxis in Chlamydomonas reinhardtii are largely unknown compared to those regulating phototaxis despite equal importance on the migratory response in the ciliated microalga. To study chemotaxis, we made a simple modification to a conventional Petri dish assay. Using the assay, a novel mechanism governing Chlamydomonas ammonium chemotaxis was revealed. First, we found that light exposure enhances the chemotactic response of wild-type Chlamydomonas strains, yet phototaxis-incompetent mutant strains, eye3-2 and ptx1, exhibit normal chemotaxis. This suggests that Chlamydomonas transduces the light signal pathway in chemotaxis differently from that in phototaxis. Second, we found that Chlamydomonas collectively migrate during chemotaxis but not phototaxis. Collective migration during chemotaxis is not clearly observed when the assay is conducted in the dark. Third, the Chlamydomonas strain CC-124 carrying agg1-, the AGGREGATE1 gene (AGG1) null mutation, exhibited a more robust collective migratory response than strains carrying the wild-type AGG1 gene. The expression of a recombinant AGG1 protein in the CC-124 strain suppressed this collective migration during chemotaxis. Altogether, these findings suggest a unique mechanism; ammonium chemotaxis in Chlamydomonas is mainly driven by collective cell migration. Furthermore, it is proposed that collective migration is enhanced by light and suppressed by the AGG1 protein.
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Affiliation(s)
- Gabela Nelson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Alexis Strain
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Atsuko Isu
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Alireza Rahnama
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Ken-Ichi Wakabayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Adam T Melvin
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
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Jia M, Munz J, Lee J, Shelley N, Xiong Y, Joo S, Jin E, Lee JH. The bHLH family NITROGEN-REPLETION INSENSITIVE1 represses nitrogen starvation-induced responses in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:337-357. [PMID: 35043510 DOI: 10.1111/tpj.15673] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Moyan Jia
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Jacob Munz
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Jenny Lee
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Nolan Shelley
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Yuan Xiong
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Sunjoo Joo
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - EonSeon Jin
- Department of Life Sciences, Research Institute for Natural Sciences, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Jae-Hyeok Lee
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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3
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Tuttle JT, Williams JR, Higgs DC. Characterization of a Chlamydomonas reinhardtii mutant strain with tolerance to low nitrogen and increased growth and biomass under nitrogen stress. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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de Carpentier F, Le Peillet J, Boisset ND, Crozet P, Lemaire SD, Danon A. Blasticidin S Deaminase: A New Efficient Selectable Marker for Chlamydomonas reinhardtii. FRONTIERS IN PLANT SCIENCE 2020; 11:242. [PMID: 32211000 PMCID: PMC7066984 DOI: 10.3389/fpls.2020.00242] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/17/2020] [Indexed: 05/21/2023]
Abstract
Chlamydomonas reinhardtii is a model unicellular organism for basic or biotechnological research, such as the production of high-value molecules or biofuels thanks to its photosynthetic ability. To enable rapid construction and optimization of multiple designs and strains, our team and collaborators have developed a versatile Chlamydomonas Modular Cloning toolkit comprising 119 biobricks. Having the ability to use a wide range of selectable markers is an important benefit for forward and reverse genetics in Chlamydomonas. We report here the development of a new selectable marker based on the resistance to the antibiotic blasticidin S, using the Bacillus cereus blasticidin S deaminase (BSR) gene. The optimal concentration of blasticidin S for effective selection was determined in both liquid and solid media and tested for multiple laboratory strains. In addition, we have shown that our new selectable marker does not interfere with other common antibiotic resistances: zeocin, hygromycin, kanamycin, paromomycin, and spectinomycin. The blasticidin resistance biobrick has been added to the Chlamydomonas Modular Cloning toolkit and is now available to the entire scientific community.
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Affiliation(s)
- Félix de Carpentier
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
- Université Paris-Saclay, Saint-Aubin, France
| | - Jeanne Le Peillet
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Nicolas D. Boisset
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
- Université Paris-Saclay, Saint-Aubin, France
| | - Pierre Crozet
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Stéphane D. Lemaire
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Antoine Danon
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
- *Correspondence: Antoine Danon,
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5
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Bogaert KA, Manoharan-Basil SS, Perez E, Levine RD, Remacle F, Remacle C. Surprisal analysis of genome-wide transcript profiling identifies differentially expressed genes and pathways associated with four growth conditions in the microalga Chlamydomonas. PLoS One 2018; 13:e0195142. [PMID: 29664904 PMCID: PMC5903653 DOI: 10.1371/journal.pone.0195142] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/16/2018] [Indexed: 12/31/2022] Open
Abstract
The usual cultivation mode of the green microalga Chlamydomonas is liquid medium and light. However, the microalga can also be grown on agar plates and in darkness. Our aim is to analyze and compare gene expression of cells cultivated in these different conditions. For that purpose, RNA-seq data are obtained from Chlamydomonas samples of two different labs grown in four environmental conditions (agar@light, agar@dark, liquid@light, liquid@dark). The RNA seq data are analyzed by surprisal analysis, which allows the simultaneous meta-analysis of all the samples. First we identify a balance state, which defines a state where the expression levels are similar in all the samples irrespectively of their growth conditions, or lab origin. In addition our analysis identifies additional constraints needed to quantify the deviation with respect to the balance state. The first constraint differentiates the agar samples versus the liquid ones; the second constraint the dark samples versus the light ones. The two constraints are almost of equal importance. Pathways involved in stress responses are found in the agar phenotype while the liquid phenotype comprises ATP and NADH production pathways. Remodeling of membrane is suggested in the dark phenotype while photosynthetic pathways characterize the light phenotype. The same trends are also present when performing purely statistical analysis such as K-means clustering and differentially expressed genes.
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Affiliation(s)
- Kenny A. Bogaert
- Theoretical Physical Chemistry, UR MOLSYS, University of Liège, Liège, Belgium
| | | | - Emilie Perez
- Genetics and Physiology of Microalgae, UR InBios, University of Liège, Liège, Belgium
| | - Raphael D. Levine
- The Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Francoise Remacle
- Theoretical Physical Chemistry, UR MOLSYS, University of Liège, Liège, Belgium
- * E-mail: (CR); (FR)
| | - Claire Remacle
- Genetics and Physiology of Microalgae, UR InBios, University of Liège, Liège, Belgium
- * E-mail: (CR); (FR)
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Nakamura H, Shiozaki T, Gonda N, Furuya K, Matsunaga S, Okada S. Utilization of ammonium by the hydrocarbon-producing microalga, Botryococcus braunii Showa. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kakinuma M, Nakamoto C, Kishi K, Coury DA, Amano H. Isolation and functional characterization of an ammonium transporter gene, PyAMT1, related to nitrogen assimilation in the marine macroalga Pyropia yezoensis (Rhodophyta). MARINE ENVIRONMENTAL RESEARCH 2017; 128:76-87. [PMID: 27581686 DOI: 10.1016/j.marenvres.2016.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 05/25/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Ammonium and nitrate are the primary nitrogen sources in natural environments, and are essential for growth and development in photosynthetic eukaryotes. In this study, we report on the isolation and characterization of an ammonium transporter gene (PyAMT1) which performs a key function in nitrogen (N) metabolism of Pyropia yezoensis thalli. The predicted length of PyAMT1 was 483 amino acids (AAs). The AA sequence included 11 putative transmembrane domains and showed approximately 33-44% identity to algal and plant AMT1 AA sequences. Functional complementation in an AMT-defective yeast mutant indicated that PyAMT1 mediated ammonium transport across the plasma membrane. Expression analysis showed that the PyAMT1 mRNA level was strongly induced by N-deficiency, and was more highly suppressed by resupply of inorganic-N than organic-N. These results suggest that PyAMT1 plays important roles in the ammonium transport system, and is highly regulated in response to external/internal N-status.
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Affiliation(s)
- Makoto Kakinuma
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan.
| | - Chika Nakamoto
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
| | - Kazuki Kishi
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
| | - Daniel A Coury
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
| | - Hideomi Amano
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
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8
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Helliwell KE, Collins S, Kazamia E, Purton S, Wheeler GL, Smith AG. Fundamental shift in vitamin B12 eco-physiology of a model alga demonstrated by experimental evolution. ISME JOURNAL 2014; 9:1446-55. [PMID: 25526368 DOI: 10.1038/ismej.2014.230] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 10/26/2014] [Accepted: 10/30/2014] [Indexed: 11/09/2022]
Abstract
A widespread and complex distribution of vitamin requirements exists over the entire tree of life, with many species having evolved vitamin dependence, both within and between different lineages. Vitamin availability has been proposed to drive selection for vitamin dependence, in a process that links an organism's metabolism to the environment, but this has never been demonstrated directly. Moreover, understanding the physiological processes and evolutionary dynamics that influence metabolic demand for these important micronutrients has significant implications in terms of nutrient acquisition and, in microbial organisms, can affect community composition and metabolic exchange between coexisting species. Here we investigate the origins of vitamin dependence, using an experimental evolution approach with the vitamin B(12)-independent model green alga Chlamydomonas reinhardtii. In fewer than 500 generations of growth in the presence of vitamin B(12), we observe the evolution of a B(12)-dependent clone that rapidly displaces its ancestor. Genetic characterization of this line reveals a type-II Gulliver-related transposable element integrated into the B(12)-independent methionine synthase gene (METE), knocking out gene function and fundamentally altering the physiology of the alga.
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Affiliation(s)
| | - Sinéad Collins
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Elena Kazamia
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Saul Purton
- Institute of Structural and Molecular Biology, UCL, London, UK
| | - Glen L Wheeler
- 1] Plymouth Marine Laboratory, Plymouth, UK [2] Marine Biological Association of UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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9
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Schmollinger S, Mühlhaus T, Boyle NR, Blaby IK, Casero D, Mettler T, Moseley JL, Kropat J, Sommer F, Strenkert D, Hemme D, Pellegrini M, Grossman AR, Stitt M, Schroda M, Merchant SS. Nitrogen-Sparing Mechanisms in Chlamydomonas Affect the Transcriptome, the Proteome, and Photosynthetic Metabolism. THE PLANT CELL 2014; 26:1410-1435. [PMID: 24748044 PMCID: PMC4036562 DOI: 10.1105/tpc.113.122523] [Citation(s) in RCA: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/19/2014] [Accepted: 03/29/2014] [Indexed: 05/17/2023]
Abstract
Nitrogen (N) is a key nutrient that limits global primary productivity; hence, N-use efficiency is of compelling interest in agriculture and aquaculture. We used Chlamydomonas reinhardtii as a reference organism for a multicomponent analysis of the N starvation response. In the presence of acetate, respiratory metabolism is prioritized over photosynthesis; consequently, the N-sparing response targets proteins, pigments, and RNAs involved in photosynthesis and chloroplast function over those involved in respiration. Transcripts and proteins of the Calvin-Benson cycle are reduced in N-deficient cells, resulting in the accumulation of cycle metabolic intermediates. Both cytosolic and chloroplast ribosomes are reduced, but via different mechanisms, reflected by rapid changes in abundance of RNAs encoding chloroplast ribosomal proteins but not cytosolic ones. RNAs encoding transporters and enzymes for metabolizing alternative N sources increase in abundance, as is appropriate for the soil environmental niche of C. reinhardtii. Comparison of the N-replete versus N-deplete proteome indicated that abundant proteins with a high N content are reduced in N-starved cells, while the proteins that are increased have lower than average N contents. This sparing mechanism contributes to a lower cellular N/C ratio and suggests an approach for engineering increased N-use efficiency.
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Affiliation(s)
- Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Timo Mühlhaus
- Molecular Biotechnology and Systems Biology, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Nanette R Boyle
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Ian K Blaby
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - David Casero
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
| | - Tabea Mettler
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Jeffrey L Moseley
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Dorothea Hemme
- Molecular Biotechnology and Systems Biology, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095
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10
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Nakhoul NL, Lee Hamm L. The challenge of determining the role of Rh glycoproteins in transport of NH3and NH4+. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/wmts.105] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nazih L. Nakhoul
- Department of Physiology; Tulane University Medical School; New Orleans LA USA
- Department of Medicine, Section of Nephrology; Tulane University Medical School; New Orleans LA USA
| | - L. Lee Hamm
- Department of Medicine, Section of Nephrology; Tulane University Medical School; New Orleans LA USA
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11
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Characterization of an ammonium transporter in the oleaginous alga Chlorella protothecoides. Appl Microbiol Biotechnol 2012; 97:919-28. [DOI: 10.1007/s00253-012-4534-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 10/18/2012] [Accepted: 10/20/2012] [Indexed: 11/26/2022]
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12
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McDonald SM, Plant JN, Worden AZ. The mixed lineage nature of nitrogen transport and assimilation in marine eukaryotic phytoplankton: a case study of micromonas. Mol Biol Evol 2010; 27:2268-83. [PMID: 20457585 PMCID: PMC2944026 DOI: 10.1093/molbev/msq113] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The prasinophyte order Mamiellales contains several widespread marine picophytoplankton (≤ 2 μm diameter) taxa, including Micromonas and Ostreococcus. Complete genome sequences are available for two Micromonas isolates, CCMP1545 and RCC299. We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed divergent types contained within each Mamiellales genome. Some were affiliated with plant and green algal AMT1 genes and others with bacterial AMT2 genes. Land plant AMT2 genes were phylogenetically closer to archaeal transporters than to Mamiellales AMT2 genes. The Mamiellales represent the first green algal genomes to harbor AMT2 genes, which are not found in Chlorella and Chlamydomonas or the chromalveolate algae analyzed but are present in oomycetes. Fewer nitrate transporter (NRT) than AMT genes were identified in the Mamiellales. NRT1 was found in all but CCMP1545 and showed highest similarity to Mamiellales and proteobacterial NRTs. NRT2 genes formed a bootstrap-supported clade basal to other green lineage organisms. Several nitrogen-related genes were colocated, forming a nitrogen gene cluster. Overall, RCC299 showed the most divergent suite of nitrogen transporters within the various Mamiellales genomes, and we developed TaqMan quantitative polymerase chain reaction primer-probes targeting a subset of these, as well as housekeeping genes, in RCC299. All those investigated showed expression either under standard growth conditions or under nitrogen depletion. Like other recent publications, our findings show a higher degree of "mixed lineage gene affiliations" among eukaryotes than anticipated, and even the most phylogenetically anomalous versions appear to be functional. Nitrogen is often considered a regulating factor for phytoplankton populations. This study provides a springboard for exploring the use and functional diversification of inorganic nitrogen transporters and related genes in eukaryotic phytoplankton.
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Inwood W, Yoshihara C, Zalpuri R, Kim KS, Kustu S. The ultrastructure of a Chlamydomonas reinhardtii mutant strain lacking phytoene synthase resembles that of a colorless alga. MOLECULAR PLANT 2008; 1:925-37. [PMID: 19825593 PMCID: PMC2902904 DOI: 10.1093/mp/ssn046] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Chlamydomonas reinhardtii strains lacking phytoene synthase, the first enzyme of carotenoid biosynthesis, are white. They lack carotenoid pigments, have very low levels of chlorophyll, and can grow only heterotrophically in the dark. Our electron and fluorescence microscopic studies showed that such a mutant strain (lts1-204) had a proliferated plastid envelope membrane but no stacks of thylakoid membranes within the plastid. It accumulated cytoplasmic compartments that appeared to be autophagous vacuoles filled with membranous material. The lts1 mutants apparently lacked pyrenoid bodies, which normally house ribulose bisphosphate carboxylase-oxygenase (Rubisco), and accumulated many starch granules. Although these mutant strains cannot synthesize the carotenoid and carotenoid-derived pigments present in the phototactic organelle (eyespot), the mutant we examined made a vestigial eyespot that was disorganized and often mislocalized to the posterior end of the cell. The absence of a pyrenoid body, the accumulation of starch, and the disorganization of the eyespot may all result from the absence of thylakoids. The ultrastructure of lts1 mutant strains is similar to but distinct from that of previously described white and yellow mutant strains of C. reinhardtii and is similar to that of naturally colorless algae of the Polytoma group.
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Affiliation(s)
- William Inwood
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720–3102, USA
| | - Corinne Yoshihara
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720–3102, USA
| | - Reena Zalpuri
- Electron Microscope Laboratory, 26 Giannini Hall, University of California, Berkeley, CA 94720–3330, USA
| | - Kwang-Seo Kim
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720–3102, USA
| | - Sydney Kustu
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720–3102, USA
- To whom correspondence should be addressed. E-mail , fax (510) 642-4995, tel. (510) 643-9308
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Yoshihara C, Inoue K, Schichnes D, Ruzin S, Inwood W, Kustu S. An Rh1-GFP fusion protein is in the cytoplasmic membrane of a white mutant strain of Chlamydomonas reinhardtii. MOLECULAR PLANT 2008; 1:1007-20. [PMID: 19825599 PMCID: PMC2902906 DOI: 10.1093/mp/ssn074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 10/14/2008] [Indexed: 05/21/2023]
Abstract
The major Rhesus (Rh) protein of the green alga Chlamydomonas reinhardtii, Rh1, is homologous to Rh proteins of humans. It is an integral membrane protein involved in transport of carbon dioxide. To localize a fusion of intact Rh1 to the green fluorescent protein (GFP), we used as host a white (lts1) mutant strain of C. reinhardtii, which is blocked at the first step of carotenoid biosynthesis. The lts1 mutant strain accumulated normal amounts of Rh1 heterotrophically in the dark and Rh1-GFP was at the periphery of the cell co-localized with the cytoplasmic membrane dye FM4-64. Although Rh1 carries a potential chloroplast targeting sequence at its N-terminus, Rh1-GFP was clearly not associated with the chloroplast envelope membrane. Moreover, the N-terminal half of the protein was not imported into chloroplasts in vitro and N-terminal regions of Rh1 did not direct import of the small subunit of ribulose bisphosphate carboxylase (SSU). Despite caveats to this interpretation, which we discuss, current evidence indicates that Rh1 is a cytoplasmic membrane protein and that Rh1-GFP is among the first cytoplasmic membrane protein fusions to be obtained in C. reinhardtii. Although lts1 (white) mutant strains cannot be used to localize proteins within sub-compartments of the chloroplast because they lack thylakoid membranes, they should nonetheless be valuable for localizing many GFP fusions in Chlamydomonas.
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Affiliation(s)
- Corinne Yoshihara
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
| | - Kentaro Inoue
- Department of Plant Sciences, 131 Asmundson Hall, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Denise Schichnes
- CNR Biological Imaging Facility, 381 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
| | - Steven Ruzin
- CNR Biological Imaging Facility, 381 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
| | - William Inwood
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
| | - Sydney Kustu
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
- To whom correspondence should be addressed. E-mail , fax (510) 642-4995, tel. (510) 643-9308
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Cherif-Zahar B, Durand A, Schmidt I, Hamdaoui N, Matic I, Merrick M, Matassi G. Evolution and functional characterization of the RH50 gene from the ammonia-oxidizing bacterium Nitrosomonas europaea. J Bacteriol 2007; 189:9090-100. [PMID: 17921289 PMCID: PMC2168606 DOI: 10.1128/jb.01089-07] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Accepted: 09/04/2007] [Indexed: 12/31/2022] Open
Abstract
The family of ammonia and ammonium channel proteins comprises the Amt proteins, which are present in all three domains of life with the notable exception of vertebrates, and the homologous Rh proteins (Rh50 and Rh30) that have been described thus far only in eukaryotes. The existence of an RH50 gene in bacteria was first revealed by the genome sequencing of the ammonia-oxidizing bacterium Nitrosomonas europaea. Here we have used a phylogenetic approach to study the evolution of the N. europaea RH50 gene, and we show that this gene, probably as a component of an integron cassette, has been transferred to the N. europaea genome by horizontal gene transfer. In addition, by functionally characterizing the Rh50(Ne) protein and the corresponding knockout mutant, we determined that NeRh50 can mediate ammonium uptake. The RH50(Ne) gene may thus have replaced functionally the AMT gene, which is missing in the genome of N. europaea and may be regarded as a case of nonorthologous gene displacement.
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16
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Ermilova EV, Nikitin MM, Fernández E. Chemotaxis to ammonium/methylammonium in Chlamydomonas reinhardtii: the role of transport systems for ammonium/methylammonium. PLANTA 2007; 226:1323-32. [PMID: 17588169 DOI: 10.1007/s00425-007-0568-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 05/25/2007] [Indexed: 05/16/2023]
Abstract
Ammonium is the preferred nitrogen source and chemoattractant for the unicellular green alga Chlamydomonas reinhardtii. Here we describe that chemotaxis to methylammonium, a non-metabolizable analogue to ammonium, that occurs only in vegetative cells and pregametes but not in gametes. A new methylammonium-resistant mutant, hat1 that was generated by insertional mutagenesis, has been isolated and found to be affected at multiple loci. At the physiological level, hat1 showed altered Km and Vmax for high-affinity ammonium and methylammonium transport. Transcript levels of the ammonium transporter genes CrAmt1.(1-8) were similar to the wild type except for a lower expression level of CrAmt1.5, 6 and 8. Treatment with the potassium-channel inhibitor tetraethylammonium (TEA) blocked chemotaxis to ammonium/methylammonium and [14C]-methylammonium uptake. Our results suggest that the hat1 mutant could be affected in genes encoding regulatory elements of AMT1 transporter activities and that chemotaxis to ammonium/methylammonium is mediated by ammonium transporters sensitive to the potassium-channel inhibitor TEA.
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Affiliation(s)
- Elena V Ermilova
- Department of Microbiology, Biological Research Institute of St. Petersburg University, Oranienbaumskoe Schosse 2, Stary Peterhof, St. Petersburg 198504, Russia.
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17
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Marino R, Melillo D, Di Filippo M, Yamada A, Pinto MR, De Santis R, Brown ER, Matassi G. Ammonium channel expression is essential for brain development and function in the larva ofCiona intestinalis. J Comp Neurol 2007; 503:135-47. [PMID: 17480017 DOI: 10.1002/cne.21370] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Ammonium uptake into the cell is known to be mediated by ammonium transport (Amt) proteins, which are present in all domains of life. The physiological role of Amt proteins remains elusive; indeed, loss-of-function experiments suggested that Amt proteins do not play an essential role in bacteria, yeast, and plants. Here we show that the reverse holds true in the tunicate Ciona intestinalis. The genome of C. intestinalis contains two AMT genes, Ci-AMT1a and Ci-AMT1b, which we show derive from an ascidian-specific gene duplication. We analyzed Ci-AMT expression during embryo development. Notably, Ci-AMT1a is expressed in the larval brain in a small number of cells defining a previously unseen V-shaped territory; these cells connect the brain cavity to the external environment. We show that the knockdown of Ci-AMT1a impairs the formation of the brain cavity and consequently the function of the otolith, the gravity-sensing organ contained in it. We speculate that the normal mechanical functioning (flotation and free movement) of the otolith may require a close regulation of ammonium salt(s) concentration in the brain cavity, because ammonium is known to affect both fluid density and viscosity; the cells forming the V territory may act as a conduit in achieving such a regulation.
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Affiliation(s)
- Rita Marino
- Stazione Zoologica A Dohrn, Villa Comunale, Napoli, Italy
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18
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Abstract
Acid-base homeostasis to a great extent relies on renal ammonia metabolism. In the past several years, seminal studies have generated important new insights into the mechanisms of renal ammonia transport. In particular, the theory that ammonia transport occurs almost exclusively through nonionic NH(3) diffusion and NH(4)(+) trapping has given way to a model postulating that a variety of proteins specifically transport NH(3) and NH(4)(+) and that this transport is critical for normal ammonia metabolism. Many of these proteins transport primarily H(+) or K(+) but also transport NH(4)(+). Nonerythroid Rh glycoproteins transport ammonia and may represent critical facilitators of ammonia transport in the kidney. This review discusses the underlying aspects of renal ammonia transport as well as specific proteins with important roles in renal ammonia transport.
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Affiliation(s)
- I. David Weiner
- Nephrology Section, North Florida/South Georgia Veterans Health System, University of Florida, Gainesville, Florida 32608
- Division of Nephrology, Hypertension and Transplantation, University of Florida, Gainesville, Florida 32608
| | - L. Lee Hamm
- Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana 70112
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19
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Kim KS, Kustu S, Inwood W. Natural history of transposition in the green alga Chlamydomonas reinhardtii: use of the AMT4 locus as an experimental system. Genetics 2006; 173:2005-19. [PMID: 16702425 PMCID: PMC1569734 DOI: 10.1534/genetics.106.058263] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Accepted: 05/10/2006] [Indexed: 11/18/2022] Open
Abstract
The AMT4 locus of the green alga Chlamydomonas reinhardtii, which we mapped to the long arm of chromosome 8, provides a good experimental system for the study of transposition. Most mutations that confer resistance to the toxic ammonium analog methylammonium are in AMT4 and a high proportion of spontaneous mutations are caused by transposon-related events. Among the 15 such events that we have characterized at the molecular level, 9 were associated with insertions of the retrotransposon TOC1, 2 with a small Gulliver-related transposon, and 1 with the Tcr1 transposon. We found that Tcr1 is apparently a foldback transposon with terminal inverted repeats that are much longer and more complex than previously realized. A duplication of Tcr1 yielded a configuration thought to be important for chromosomal evolution. Other mutations in AMT4 were caused by two mobile elements that have not been described before. The sequence of one, which we propose to call the Bill element, indicates that it probably transposes by way of a DNA intermediate and requires functions that it does not encode. The sequence of the other and bioinformatic analysis indicates that it derives from a miniature retrotransposon or TRIM, which we propose to call MRC1 (miniature retrotransposon of Chlamydomonas).
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Affiliation(s)
- Kwang-Seo Kim
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
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20
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Cheng L, Zhang L, Chen H, Gao C. Carbon dioxide removal from air by microalgae cultured in a membrane-photobioreactor. Sep Purif Technol 2006. [DOI: 10.1016/j.seppur.2005.12.006] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Ji Q, Hashmi S, Liu Z, Zhang J, Chen Y, Huang CH. CeRh1 (rhr-1) is a dominant Rhesus gene essential for embryonic development and hypodermal function in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2006; 103:5881-6. [PMID: 16595629 PMCID: PMC1458667 DOI: 10.1073/pnas.0600901103] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Indexed: 01/16/2023] Open
Abstract
Rhesus (Rh) proteins share a conserved 12-transmembrane topology and specify a family of putative CO(2) channels found in diverse species from microbes to human, but their functional essentiality and physiological importance in metazoans is unknown. To address this key issue and analyze Rh-engaged physiologic processes, we sought to explore model organisms with fewer Rh genes yet are tractable to genetic manipulations. In this article, we describe the identification in nematodes of two Rh homologues that are highly conserved and similar to human Rh glycoproteins, and we focus on their characterization in Caenorhabditis elegans. RNA analysis revealed that CeRh1 is abundantly expressed in all developmental stages, with highest levels in adults, whereas CeRh2 shows a differential and much lower expression pattern. In transient expression in human cells, both CeRh1 and CeRh2-GFP fusion proteins were routed to the plasma membrane. Transgenic analysis with GFP or LacZ-fusion reporters showed that CeRh1 is mainly expressed in hypodermal tissue, although it is also in other cell types. Mutagenesis analysis using deletion constructs mapped a minimal promoter region driving CeRh1 gene expression. Although CeRh2 was dispensable, RNA interference with CeRh1 caused a lethal phenotype mainly affecting late stages of C. elegans embryonic development, which could be rescued by the CbRh1 homologue from the worm Caenorhabditis briggsae. Taken together, our data provide direct evidence for the essentiality of the CeRh1 gene in C. elegans, establishing a useful animal model for investigating CO(2) channel function by cross-species complementation.
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Affiliation(s)
- Qiongmei Ji
- Laboratories of *Biochemistry and Molecular Genetics
| | - Sarwar Hashmi
- Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, 310 East 67th Street, New York, NY 10021
| | - Zhi Liu
- Laboratories of *Biochemistry and Molecular Genetics
| | - Jun Zhang
- Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, 310 East 67th Street, New York, NY 10021
| | - Ying Chen
- Laboratories of *Biochemistry and Molecular Genetics
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22
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Bakouh N, Benjelloun F, Cherif-Zahar B, Planelles G. The challenge of understanding ammonium homeostasis and the role of the Rh glycoproteins. Transfus Clin Biol 2006; 13:139-46. [PMID: 16564724 DOI: 10.1016/j.tracli.2006.02.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rh glycoproteins belong to the superfamily of ammonium transporters, but until recent functional studies their functional role was unknown. This review focuses on the functional results obtained in our laboratory after the heterologous expression of RhAG (the erythroid Rh glycoprotein) and RhCG (an epithelial Rh glycoprotein). RhAG and RhCG were expressed in two different expression systems (HeLa cells and Xenopus laevis oocytes) that differed in their endogenous membrane permeabilities for NH3 and NH4+. To check if RhAG and RhCG are ammonium transporters, we measured intracellular pH changes in cells exposed to an ammonium-containing solution, and analyzed the ammonium-induced NH3 and NH4+ transmembrane fluxes in control versus transfected cells. We observed that RhAG and RhCG expression induced an enhancement of the ammonium-induced initial alkalinization (related to NH3 influx into the cell) and secondary acidification (related to NH4+ influx into the cell). Moreover, sub-millimolar ammonium concentrations induced inward currents in voltage-clamped RhAG- and in RhCG-expressing oocytes. Taken together, these results show not only that RhAG and RhCG are ammonium transporters, but also that they are promoting the transmembrane transport of NH3 and of NH4+. Data from our laboratory and from other groups raise several questions that are discussed.
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Affiliation(s)
- N Bakouh
- Inserm U 806, université René-Descartes-Paris 5, faculté de médecine-Paris 5, 156, rue de Vaugirard, 75730 Paris cedex 15, France
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23
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Peng J, Huang CH. Rh proteins vs Amt proteins: an organismal and phylogenetic perspective on CO2 and NH3 gas channels. Transfus Clin Biol 2006; 13:85-94. [PMID: 16564193 DOI: 10.1016/j.tracli.2006.02.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Rh (Rhesus) proteins are homologues of ammonium transport (Amt) proteins. Physiological and structural evidence shows that Amt proteins are gas channels for NH(3), but the substrate of Rh proteins, be it CO2 as shown in green alga, or NH3/NH4+ as shown in mammalian cells, remains disputed. We assembled a large dataset generated of Rh and Amt to explore how Rh originated from and evolved independently of Amt relatives. Analysis of this rich data implies that Rh was split from Amt first to emerge in archaeal species. The Rh ancestor underwent divergence and duplication along speciation, leading to neofunctionalization and subfunctionalization of the Rh family. The characteristic organismal distribution of Rh vs. Amt reflects their early separation and subsequent independent evolution: they coexist in microbes and invertebrates but do not in fungi, vascular plants or vertebrates. Rh gene-duplication was prominent in vertebrates: while epithelial RhBG/RhCG displayed strong purifying selection, erythroid Rh30 and RhAG experienced different episodes of positive selection in each of which adaptive evolution occurred at certain time points and in a few codon sites. Mammalian Rh30 and RhAG were subject to particularly strong positive selection in some codon sites in the lineage from rodents to human. The grounds of this adaptive evolution may be driven by the necessity to increase the surface/volume ratio of biconcave erythrocytes for facilitative gas diffusion. Altogether, these results are consistent with Rh proteins not being the orthologue of Amt proteins but having gained the function for CO2/HCO3- transport, with important roles in systemic pH regulation.
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Affiliation(s)
- J Peng
- Laboratory of Biochemistry and Molecular Genetics, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10021, USA
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24
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Kustu S, Inwood W. Biological gas channels for NH3 and CO2: evidence that Rh (Rhesus) proteins are CO2 channels. Transfus Clin Biol 2006; 13:103-10. [PMID: 16563833 DOI: 10.1016/j.tracli.2006.03.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Physiological evidence from our laboratory indicates that Amt/Mep proteins are gas channels for NH3, the first biological gas channels to be described. This view has now been confirmed by structural evidence and is displacing the previous belief that Amt/Mep proteins were active transporters for the NH4+ ion. Still disputed is the physiological substrate for Rh proteins, the only known homologues of Amt/Mep proteins. Many think they are mammalian ammonium (NH4+ or NH3) transporters. Following Monod's famous dictum, "Anything found to be true of E. coli must also be true of elephants" [Perspect. Biol. Med. 47(1) (2004) 47], we explored the substrate for Rh proteins in the unicellular green alga Chlamydomonas reinhardtii. C. reinhardtii is one of the simplest organisms to have Rh proteins and it also has Amt proteins. Physiological studies in this microbe indicate that the substrate for Rh proteins is CO2 and confirm that the substrate for Amt proteins is NH3. Both are readily hydrated gases. Knowing that transport of CO2 is the ancestral function of Rh proteins supports the inference from hematological research that a newly evolving role of the human Rh30 proteins, RhCcEe and RhD, is to help maintain the flexible, flattened shape of the red cell.
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Affiliation(s)
- S Kustu
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, Berkeley, CA 94720-3102, USA.
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25
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Huang CH, Peng J. Evolutionary conservation and diversification of Rh family genes and proteins. Proc Natl Acad Sci U S A 2005; 102:15512-7. [PMID: 16227429 PMCID: PMC1266151 DOI: 10.1073/pnas.0507886102] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Indexed: 11/18/2022] Open
Abstract
Rhesus (Rh) proteins were first identified in human erythroid cells and recently in other tissues. Like ammonia transporter (Amt) proteins, their only homologues, Rh proteins have the 12 transmembrane-spanning segments characteristic of transporters. Many think Rh and Amt proteins transport the same substrate, NH(3)/NH(4)(+), whereas others think that Rh proteins transport CO(2) and Amt proteins NH(3). In the latter view, Rh and Amt are different biological gas channels. To reconstruct the phylogeny of the Rh family and study its coexistence with and relationship to Amt in depth, we analyzed 111 Rh genes and 260 Amt genes. Although Rh and Amt are found together in organisms as diverse as unicellular eukaryotes and sea squirts, Rh genes apparently arose later, because they are rare in prokaryotes. However, Rh genes are prominent in vertebrates, in which Amt genes disappear. In organisms with both types of genes, Rh had apparently diverged away from Amt rapidly and then evolved slowly over a long period. Functionally divergent amino acid sites are clustered in transmembrane segments and around the gas-conducting lumen recently identified in Escherichia coli AmtB, in agreement with Rh proteins having new substrate specificity. Despite gene duplications and mutations, the Rh paralogous groups all have apparently been subject to strong purifying selection indicating functional conservation. Genes encoding the classical Rh proteins in mammalian red cells show higher nucleotide substitution rates at nonsynonymous codon positions than other Rh genes, a finding that suggests a possible role for these proteins in red cell morphogenetic evolution.
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Affiliation(s)
- Cheng-Han Huang
- Laboratory of Biochemistry and Molecular Genetics, Lindsley F. Kimball Research Institute, New York Blood Center, 310 East 67th Street, New York, NY 10021, USA.
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