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Patra N, Hariharan S, Gain H, Maiti MK, Das A, Banerjee J. TypiCal but DeliCate Ca ++re: Dissecting the Essence of Calcium Signaling Network as a Robust Response Coordinator of Versatile Abiotic and Biotic Stimuli in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:752246. [PMID: 34899779 PMCID: PMC8655846 DOI: 10.3389/fpls.2021.752246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/27/2021] [Indexed: 06/14/2023]
Abstract
Plant growth, development, and ultimately crop productivity are largely impacted by the interaction of plants with different abiotic and biotic factors throughout their life cycle. Perception of different abiotic stresses, such as salt, cold, drought, heat, and heavy metals, and interaction with beneficial and harmful biotic agents by plants lead to transient, sustained, or oscillatory changes of [calcium ion, Ca2+]cyt within the cell. Significant progress has been made in the decoding of Ca2+ signatures into downstream responses to modulate differential developmental and physiological responses in the whole plant. Ca2+ sensor proteins, mainly calmodulins (CaMs), calmodulin-like proteins (CMLs), and others, such as Ca2+-dependent protein kinases (CDPKs), calcineurin B-like proteins (CBLs), and calmodulin-binding transcription activators (CAMTAs) have played critical roles in coupling the specific stress stimulus with an appropriate response. This review summarizes the current understanding of the Ca2+ influx and efflux system in plant cells and various Ca2+ binding protein-mediated signal transduction pathways that are delicately orchestrated to mitigate abiotic and biotic stresses. The probable interactions of different components of Ca2+ sensor relays and Ca2+ sensor responders in response to various external stimuli have been described diagrammatically focusing on established pathways and latest developments. Present comprehensive insight into key components of the Ca2+ signaling toolkit in plants can provide an innovative framework for biotechnological manipulations toward crop improvability in near future.
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Affiliation(s)
- Neelesh Patra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Shruthi Hariharan
- Agricultural and Food Engineering Department, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Hena Gain
- Agricultural and Food Engineering Department, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Mrinal K. Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Arpita Das
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Joydeep Banerjee
- Agricultural and Food Engineering Department, Indian Institute of Technology Kharagpur, Kharagpur, India
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Izquieta-Rojano S, López-Aizpún M, Irigoyen JJ, Santamaría JM, Santamaría C, Lasheras E, Ochoa-Hueso R, Elustondo D. Eco-physiological response of Hypnum cupressiforme Hedw. to increased atmospheric ammonia concentrations in a forest agrosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 619-620:883-895. [PMID: 29734634 DOI: 10.1016/j.scitotenv.2017.11.139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/20/2017] [Accepted: 11/13/2017] [Indexed: 06/08/2023]
Abstract
Ammonia (NH3) emissions are linked to eutrophication, plant toxicity and ecosystem shifts from N to P limitation. Bryophytes are key components of terrestrial ecosystems, yet highly sensitive to N deposition. Hence, physiological responses of mosses may be indicative of NH3-related impacts, and thus useful to foresee future ecosystem damages and establish atmospheric Critical Levels (CLEs). In this work, samples of Hypnum cupressiforme Hedw. were seasonally collected along a well-defined NH3 concentration gradient in an oak woodland during a one-year period. We performed a comprehensive evaluation of tissue chemistry, stoichiometry, metabolic enzymes, antioxidant response, membrane damages, photosynthetic pigments, soluble protein content and N and C isotopic fractionation. Our results showed that all the physiological parameters studied (except P, K, Ca and C) responded to the NH3 gradient in predictable ways, although the magnitude and significance of the response were dependent on the sampling season, especially for enzymatic activities and pigments content. Nutritional imbalances, membrane damages and disturbance of cellular C and N metabolism were found as a consequence to NH3 exposure, being more affected the mosses more exposed to the barn atmosphere. These findings suggested significant implications of intensive farming for the correct functioning of oak woodlands and highlighted the importance of seasonal dynamics in the study of key physiological processes related to photosynthesis, mosses nutrition and responses to oxidative stress. Finally, tissue N showed the greatest potential for the identification of NH3-related ecological end points (estimated CLE=3.5μgm-3), whereas highly scattered physiological responses, although highly sensitive, were not suitable to that end.
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Affiliation(s)
- S Izquieta-Rojano
- Universidad de Navarra, Facultad de Ciencias, Departamento de Química, Laboratorio Integrado de Calidad Ambiental (LICA), Campus Universitario, Irunlarrea 1, 31008 Pamplona, Spain
| | - M López-Aizpún
- Universidad de Navarra, Facultad de Ciencias, Departamento de Química, Laboratorio Integrado de Calidad Ambiental (LICA), Campus Universitario, Irunlarrea 1, 31008 Pamplona, Spain
| | - J J Irigoyen
- Universidad de Navarra, Facultad de Ciencias, Departamento de Biología Ambiental, Campus Universitario, Irunlarrea 1, 31008 Pamplona, Spain
| | - J M Santamaría
- Universidad de Navarra, Facultad de Ciencias, Departamento de Química, Laboratorio Integrado de Calidad Ambiental (LICA), Campus Universitario, Irunlarrea 1, 31008 Pamplona, Spain.
| | - C Santamaría
- Universidad de Navarra, Facultad de Ciencias, Departamento de Química, Laboratorio Integrado de Calidad Ambiental (LICA), Campus Universitario, Irunlarrea 1, 31008 Pamplona, Spain
| | - E Lasheras
- Universidad de Navarra, Facultad de Ciencias, Departamento de Química, Laboratorio Integrado de Calidad Ambiental (LICA), Campus Universitario, Irunlarrea 1, 31008 Pamplona, Spain
| | - R Ochoa-Hueso
- Universidad Autónoma de Madrid, Departmento de Ecología, Darwin 2, 28049 Madrid, Spain
| | - D Elustondo
- Universidad de Navarra, Facultad de Ciencias, Departamento de Química, Laboratorio Integrado de Calidad Ambiental (LICA), Campus Universitario, Irunlarrea 1, 31008 Pamplona, Spain
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Khraiwesh B, Qudeimat E, Thimma M, Chaiboonchoe A, Jijakli K, Alzahmi A, Arnoux M, Salehi-Ashtiani K. Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response. Sci Rep 2015; 5:17434. [PMID: 26615914 PMCID: PMC4663497 DOI: 10.1038/srep17434] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/29/2015] [Indexed: 12/22/2022] Open
Abstract
Changes in the environment, such as those caused by climate change, can exert stress
on plant growth, diversity and ultimately global food security. Thus, focused
efforts to fully understand plant response to stress are urgently needed in order to
develop strategies to cope with the effects of climate change. Because
Physcomitrella patens holds a key evolutionary position bridging the gap
between green algae and higher plants, and because it exhibits a well-developed
stress tolerance, it is an excellent model for such exploration. Here, we have used
Physcomitrella patens to study genome-wide responses to abiotic stress
through transcriptomic analysis by a high-throughput sequencing platform. We report
a comprehensive analysis of transcriptome dynamics, defining profiles of elicited
gene regulation responses to abiotic stress-associated hormone Abscisic Acid (ABA),
cold, drought, and salt treatments. We identified more than 20,000 genes expressed
under each aforementioned stress treatments, of which 9,668 display differential
expression in response to stress. The comparison of Physcomitrella patens
stress regulated genes with unicellular algae, vascular and flowering plants
revealed genomic delineation concomitant with the evolutionary movement to land,
including a general gene family complexity and loss of genes associated with
different functional groups.
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Affiliation(s)
- Basel Khraiwesh
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, KSA
| | - Enas Qudeimat
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, KSA
| | - Manjula Thimma
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, KSA
| | - Amphun Chaiboonchoe
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Kenan Jijakli
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Amnah Alzahmi
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Marc Arnoux
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
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Zeng H, Xu L, Singh A, Wang H, Du L, Poovaiah BW. Involvement of calmodulin and calmodulin-like proteins in plant responses to abiotic stresses. FRONTIERS IN PLANT SCIENCE 2015; 6:600. [PMID: 26322054 PMCID: PMC4532166 DOI: 10.3389/fpls.2015.00600] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 07/20/2015] [Indexed: 05/18/2023]
Abstract
Transient changes in intracellular Ca(2+) concentration have been well recognized to act as cell signals coupling various environmental stimuli to appropriate physiological responses with accuracy and specificity in plants. Calmodulin (CaM) and calmodulin-like proteins (CMLs) are major Ca(2+) sensors, playing critical roles in interpreting encrypted Ca(2+) signals. Ca(2+)-loaded CaM/CMLs interact and regulate a broad spectrum of target proteins such as channels/pumps/antiporters for various ions, transcription factors, protein kinases, protein phosphatases, metabolic enzymes, and proteins with unknown biochemical functions. Many of the target proteins of CaM/CMLs directly or indirectly regulate plant responses to environmental stresses. Basic information about stimulus-induced Ca(2+) signal and overview of Ca(2+) signal perception and transduction are briefly discussed in the beginning of this review. How CaM/CMLs are involved in regulating plant responses to abiotic stresses are emphasized in this review. Exciting progress has been made in the past several years, such as the elucidation of Ca(2+)/CaM-mediated regulation of AtSR1/CAMTA3 and plant responses to chilling and freezing stresses, Ca(2+)/CaM-mediated regulation of CAT3, MAPK8 and MKP1 in homeostasis control of reactive oxygen species signals, discovery of CaM7 as a DNA-binding transcription factor regulating plant response to light signals. However, many key questions in Ca(2+)/CaM-mediated signaling warrant further investigation. Ca(2+)/CaM-mediated regulation of most of the known target proteins is presumed based on their interaction. The downstream targets of CMLs are mostly unknown, and how specificity of Ca(2+) signaling could be realized through the actions of CaM/CMLs and their target proteins is largely unknown. Future breakthroughs in Ca(2+)/CaM-mediated signaling will not only improve our understanding of how plants respond to environmental stresses, but also provide the knowledge base to improve stress-tolerance of crops.
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Affiliation(s)
- Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Luqin Xu
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Amarjeet Singh
- Laboratory of Molecular Plant Science, Department of Horticulture, Washington State University, PullmanWA, USA
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Liqun Du
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - B. W. Poovaiah
- Laboratory of Molecular Plant Science, Department of Horticulture, Washington State University, PullmanWA, USA
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Richardt S, Timmerhaus G, Lang D, Qudeimat E, Corrêa LGG, Reski R, Rensing SA, Frank W. Microarray analysis of the moss Physcomitrella patens reveals evolutionarily conserved transcriptional regulation of salt stress and abscisic acid signalling. PLANT MOLECULAR BIOLOGY 2010; 72:27-45. [PMID: 19806323 DOI: 10.1007/s11103-009-9550-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Accepted: 09/03/2009] [Indexed: 05/03/2023]
Abstract
Regulatory networks of salt stress and abscisic acid (ABA) responses have previously been analyzed in seed plants. Here, we report microarray expression profiles of 439 genes encoding transcription-associated proteins (TAPs) in response to salt stress and ABA in the salt-tolerant moss Physcomitrella patens. Fourteen and 56 TAP genes were differentially expressed within 60 min of NaCl and ABA treatment, respectively, indicating that these responses are regulated at the transcriptional level. Overlapping expression profiles, as well as the up-regulation of ABA biosynthesis genes, suggest that ABA mediates the salt stress responses in P. patens. Comparison to public gene expression data of Arabidopsis thaliana and phylogenetic analyses suggest that the role of DREB-like, Dof, and bHLH TAPs in salt stress responses have been conserved during embryophyte evolution, and that the function of ABI3-like, bZIP, HAP3, and CO-like TAPs in seed development and flowering emerged from pre-existing ABA and light signalling pathways.
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Affiliation(s)
- Sandra Richardt
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
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Li C, Xie W, Bai W, Li Z, Zhao Y, Liu H. Calmodulin binds to maize lipid transfer protein and modulates its lipids binding ability. FEBS J 2008; 275:5298-308. [DOI: 10.1111/j.1742-4658.2008.06660.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wang X, Liu Z, He Y. Responses and tolerance to salt stress in bryophytes. PLANT SIGNALING & BEHAVIOR 2008; 3:516-8. [PMID: 19513243 PMCID: PMC2634484 DOI: 10.4161/psb.3.8.6337] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 05/27/2008] [Indexed: 05/09/2023]
Abstract
During exposure to salt environments, plants could perceive salt signal and transmit the signal to cellular machinery to activate adaptive responses. In bryophytes, salt signal components and transcript factor identified suggest that salt activate adaptive responses to tolerate adverse environments. The ability of bryophytes to tolerate salt is determined by multiple biochemical pathways. Transmembrane transport proteins that mediate ion fluxes play a curial role in ionic and osmotic homeostasis under salt environments. Defense proteins protect cells from denaturation and degradation, as well as from oxidative damage following exposure to salt stress in bryophytes. ABA and salt stress positively affect the expression of common genes that participate in protection plant cells from injure, and ABA may be responsible for the ability to tolerate salt stress in bryophytes. In this paper, we reveal the mechanisms of salt responses and tolerance in bryophytes, and imply conservation between higher plants and bryophytes in response and tolerance to salt stress.
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Affiliation(s)
- Xiaoqin Wang
- College of Life Sciences; Capital Normal University; Beijing, China
- College of Life Sciences; Xiamen University; Xiamen, China
| | - Zheng Liu
- Department of Plant Sciences; University of Cambridge; Cambridge, United Kingdom
| | - Yikun He
- College of Life Sciences; Capital Normal University; Beijing, China
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Rensing SA, Ick J, Fawcett JA, Lang D, Zimmer A, Van de Peer Y, Reski R. An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol Biol 2007; 7:130. [PMID: 17683536 PMCID: PMC1952061 DOI: 10.1186/1471-2148-7-130] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Accepted: 08/02/2007] [Indexed: 11/13/2022] Open
Abstract
Background: Analyses of complete genomes and large collections of gene transcripts have shown that most, if not all seed plants have undergone one or more genome duplications in their evolutionary past. Results: In this study, based on a large collection of EST sequences, we provide evidence that the haploid moss Physcomitrella patens is a paleopolyploid as well. Based on the construction of linearized phylogenetic trees we infer the genome duplication to have occurred between 30 and 60 million years ago. Gene Ontology and pathway association of the duplicated genes in P. patens reveal different biases of gene retention compared with seed plants. Conclusion: Metabolic genes seem to have been retained in excess following the genome duplication in P. patens. This might, at least partly, explain the versatility of metabolism, as described for P. patens and other mosses, in comparison to other land plants.
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Affiliation(s)
- Stefan A Rensing
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, D-79104 Freiburg, Germany
| | - Julia Ick
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, D-79104 Freiburg, Germany
| | - Jeffrey A Fawcett
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, D-79104 Freiburg, Germany
| | - Andreas Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, D-79104 Freiburg, Germany
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, D-79104 Freiburg, Germany
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Cuming AC, Cho SH, Kamisugi Y, Graham H, Quatrano RS. Microarray analysis of transcriptional responses to abscisic acid and osmotic, salt, and drought stress in the moss, Physcomitrella patens. THE NEW PHYTOLOGIST 2007; 176:275-287. [PMID: 17696978 DOI: 10.1111/j.1469-8137.2007.02187.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Dehydration tolerance was an adaptive trait necessary for the colonization of land by plants, and remains widespread among bryophytes: the nearest extant relatives of the first land plants. A genome-wide analysis was undertaken of water-stress responses in the model moss Physcomitrella patens to identify stress-responsive genes. An oligonucleotide microarray was used for transcriptomic analysis of Physcomitrella treated with abscisic acid (ABA), or subjected to osmotic, salt and drought stress. Bioinformatic analysis of the Physcomitrella genome identified the responsive genes, and a number of putative stress-related cis-regulatory elements. In protonemal tissue, 130 genes were induced by dehydration, 56 genes by ABA, but only 10 and eight genes, respectively, by osmotic and salt stress. Fifty-one genes were induced by more than one treatment. Seventy-six genes, principally encoding chloroplast proteins, were drought down-regulated. Many ABA- and drought-responsive genes are homologues of angiosperm genes expressed during drought stress and seed development. These ABA- and drought-responsive genes include those encoding a number of late embryogenesis abundant (LEA) proteins, a 'DREB' transcription factor and a Snf-related kinase homologous with the Arabidopsis ABA signal transduction component 'OPEN STOMATA 1'. Evolutionary capture of conserved stress-regulatory transcription factors by the seed developmental pathway probably accounts for the seed-specificity of desiccation tolerance among angiosperms.
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Affiliation(s)
- Andrew C Cuming
- Centre for Plant Science, University of Leeds, Leeds LS2 9JT, UK
| | - Sung Hyun Cho
- Department of Biology, 1 Brookings Drive, Washington University, St. Louis, MO 63130-4899, USA
| | - Yasuko Kamisugi
- Centre for Plant Science, University of Leeds, Leeds LS2 9JT, UK
| | - Helen Graham
- Centre for Plant Science, University of Leeds, Leeds LS2 9JT, UK
| | - Ralph S Quatrano
- Department of Biology, 1 Brookings Drive, Washington University, St. Louis, MO 63130-4899, USA
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Lang D, Eisinger J, Reski R, Rensing SA. Representation and high-quality annotation of the Physcomitrella patens transcriptome demonstrates a high proportion of proteins involved in metabolism in mosses. PLANT BIOLOGY (STUTTGART, GERMANY) 2005; 7:238-50. [PMID: 15912443 DOI: 10.1055/s-2005-837578] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
To gain insight into the transcriptome of the well-used plant model system Physcomitrella patens, several EST sequencing projects have been undertaken. We have clustered, assembled, and annotated all publicly available EST and CDS sequences in order to represent the transcriptome of this non-seed plant. Here, we present our fully annotated knowledge resource for the Physcomitrella patens transcriptome, integrating annotation from the production process of the clustered sequences and from a high-quality annotation pipeline developed during this study. Each transcript is represented as an entity containing full annotations and GO term associations. The whole production, filtering, clustering, and annotation process is being modelled and results in seven datasets, representing the annotated Physcomitrella transcriptome from different perspectives. We were able to annotate 63.4 % of the 26 123 virtual transcripts. The transcript archetype, as covered by our clustered data, is compared to a compilation based on all available Physcomitrella full length CDS. The distribution of the gene ontology annotations (GOA) for the virtual transcriptome of Physcomitrella patens demonstrates consistency in the ratios of the core molecular functions among the plant GOA. However, the metabolism subcategory is over-represented in bryophytes as compared to seed plants. This observation can be taken as an indicator for the wealth of alternative metabolic pathways in moss in comparison to spermatophytes. All resources presented in this study have been made available to the scientific community through a suite of user-friendly web interfaces via www.cosmoss.org and form the basis for assembly and annotation of the moss genome, which will be sequenced in 2005.
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Affiliation(s)
- D Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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Rensing SA, Fritzowsky D, Lang D, Reski R. Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens. BMC Genomics 2005; 6:43. [PMID: 15784153 PMCID: PMC1079823 DOI: 10.1186/1471-2164-6-43] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Accepted: 03/22/2005] [Indexed: 11/18/2022] Open
Abstract
Background The moss Physcomitrella patens is an emerging plant model system due to its high rate of homologous recombination, haploidy, simple body plan, physiological properties as well as phylogenetic position. Available EST data was clustered and assembled, and provided the basis for a genome-wide analysis of protein encoding genes. Results We have clustered and assembled Physcomitrella patens EST and CDS data in order to represent the transcriptome of this non-seed plant. Clustering of the publicly available data and subsequent prediction resulted in a total of 19,081 non-redundant ORF. Of these putative transcripts, approximately 30% have a homolog in both rice and Arabidopsis transcriptome. More than 130 transcripts are not present in seed plants but can be found in other kingdoms. These potential "retained genes" might have been lost during seed plant evolution. Functional annotation of these genes reveals unequal distribution among taxonomic groups and intriguing putative functions such as cytotoxicity and nucleic acid repair. Whereas introns in the moss are larger on average than in the seed plant Arabidopsis thaliana, position and amount of introns are approximately the same. Contrary to Arabidopsis, where CDS contain on average 44% G/C, in Physcomitrella the average G/C content is 50%. Interestingly, moss orthologs of Arabidopsis genes show a significant drift of codon fraction usage, towards the seed plant. While averaged codon bias is the same in Physcomitrella and Arabidopsis, the distribution pattern is different, with 15% of moss genes being unbiased. Species-specific, sensitive and selective splice site prediction for Physcomitrella has been developed using a dataset of 368 donor and acceptor sites, utilizing a support vector machine. The prediction accuracy is better than those achieved with tools trained on Arabidopsis data. Conclusion Analysis of the moss transcriptome displays differences in gene structure, codon and splice site usage in comparison with the seed plant Arabidopsis. Putative retained genes exhibit possible functions that might explain the peculiar physiological properties of mosses. Both the transcriptome representation (including a BLAST and retrieval service) and splice site prediction have been made available on , setting the basis for assembly and annotation of the Physcomitrella genome, of which draft shotgun sequences will become available in 2005.
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Affiliation(s)
- Stefan A Rensing
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Dana Fritzowsky
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
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Wang Z, Xie W, Chi F, Li C. Identification of non-specific lipid transfer protein-1 as a calmodulin-binding protein inArabidopsis. FEBS Lett 2005; 579:1683-7. [PMID: 15757661 DOI: 10.1016/j.febslet.2005.02.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Revised: 01/24/2005] [Accepted: 02/06/2005] [Indexed: 10/25/2022]
Abstract
Although non-specific lipid transfer proteins (nsLTPs) are widely present in plants, their functions and regulations have not been fully understood. In this report, Arabidopsis nsLTP1 was cloned and expressed to investigate its binding to calmodulin (CaM). Gel overlay assays revealed that recombinant nsLTP1 bound to CaM in a calcium-independent manner. The association of nsLTP1 and CaM was corroborated using CaM-Sepharose beads to specifically isolate recombinant nsLTP1 from crude bacterial lysate. The CaM-binding site was mapped in nsLTP1 to the region of 69-80 amino acids. This region is highly conserved among plant nsLTPs, implicating that nsLTPs are a new family of CaM-binding proteins whose functions may be mediated by CaM signaling.
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Affiliation(s)
- Zhe Wang
- Department of Biochemistry and Molecular Biology, Nankai University, Tianjin 300071, PR China
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Minami A, Nagao M, Ikegami K, Koshiba T, Arakawa K, Fujikawa S, Takezawa D. Cold acclimation in bryophytes: low-temperature-induced freezing tolerance in Physcomitrella patens is associated with increases in expression levels of stress-related genes but not with increase in level of endogenous abscisic acid. PLANTA 2005; 220:414-23. [PMID: 15349781 DOI: 10.1007/s00425-004-1361-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Accepted: 06/24/2004] [Indexed: 05/05/2023]
Abstract
Bryophyte species growing in areas in which temperatures fall below zero in winter are likely to have tolerance to freezing stress. It is well established in higher plants that freezing tolerance is acquired by exposure to non-freezing low temperatures, accompanied by expression of various genes and increases in levels of the stress hormone abscisic acid (ABA). However, little is known about the physiological changes induced by cold acclimation in non-vascular plants such as bryophytes. We examined the effects of low temperatures on protonema cells of the moss Physcomitrella patens (Hedw.) Bruch and Schimp. The freezing tolerance of protonema cells was clearly increased by incubation at low temperatures ranging from 10 degrees C to 0 degrees C, with maximum tolerance achieved by incubation at 0 degrees C for several days. The enhancement of freezing tolerance by low temperatures occurred in both light and dark conditions and was accompanied by accumulation of several transcripts for late-embryogenesis-abundant (LEA) proteins and boiling-soluble proteins. By de-acclimation, low-temperature-induced expression of these transcripts and proteins, as well as the freezing tolerance, was reduced. Interestingly, endogenous levels of ABA in tissues or that secreted into the culture medium were not specifically increased by low-temperature treatment. Furthermore, removal of ABA from the medium by addition of activated charcoal did not affect low-temperature-induced freezing tolerance of the protonema cells. Our results provide evidence that bryophytes have an ABA-independent cold-signaling pathway leading to expression of stress-related genes and resultant acquisition of freezing tolerance.
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Affiliation(s)
- Anzu Minami
- Institute of Low Temperature Science, Hokkaido University, 060-0819 Sapporo, Japan
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Bouché N, Yellin A, Snedden WA, Fromm H. Plant-specific calmodulin-binding proteins. ANNUAL REVIEW OF PLANT BIOLOGY 2005; 56:435-66. [PMID: 15862103 DOI: 10.1146/annurev.arplant.56.032604.144224] [Citation(s) in RCA: 257] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Calmodulin CaM is the most prominent Ca2+ transducer in eukaryotic cells, regulating the activity of numerous proteins with diverse cellular functions. Many features of CaM and its downstream targets are similar in plants and other eukaryotes. However, plants possess a unique set of CaM-related proteins, and several unique CaM target proteins. This review discusses recent progress in identifying plant-specific CaM-binding proteins and their roles in response to biotic and abiotic stresses and development. The review also addresses aspects emerging from recent structural studies of CaM interactions with target proteins relevant to plants.
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Affiliation(s)
- Nicolas Bouché
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Laboratoire de Biologie Cellulaire, 78026 Versailles, France.
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