Identification of Nostoc punctiforme akinete-expressed genes using differential display.
TL;DR: To identify genes associated with akinete development, differential display was used to amplify and compare cDNA from a wild‐type and zwf mutant strain of N. punctiforme following a switch to dark heterotrophic conditions and three novel akinete‐expressed genes were identified.
Abstract: Akinetes are spore-like resting cells formed by certain filamentous cyanobacteria that have increased resistance to environmental stress. They can be found at low frequencies in dense cultures experiencing low light or phosphate limitation, but also form at high frequencies in a zwf mutant strain of Nostoc punctiforme following dark incubation in the presence of fructose. The wild-type strain is capable of facultative heterotrophic growth under these conditions and does not form akinetes. To identify genes associated with akinete development, differential display was used to amplify and compare cDNA from a wild-type and zwf mutant strain of N. punctiforme following a switch to dark heterotrophic conditions. Screening of candidate genes by reverse transcriptase real-time quantitative PCR and subsequent testing for akinete-specific expression using GFP transcriptional reporter plasmids lead to the identification of three novel akinete-expressed genes. The genes identified from the screening encoded for proteins homologous to an aminopeptidase (aapN), a zinc protease (hap) and an ATP-binding cassette (ABC)-type transporter (aet). Expression of hap was also increased in developing hormogonia, a transient type of differentiated filament capable of gliding motility. Transcriptional start sites for akinete-expressed genes were determined using random amplification of cDNA ends (RACE), and promoter regions were compared with orthologues in other filamentous cyanobacteria to identify putative regulatory sequences.
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TL;DR: This Review addresses cyanob bacterial intercellular communication, the supracellular structure of the cyanobacterial filament and the basic principles that govern the process of heterocyst differentiation.
Abstract: Within the wide biodiversity that is found in the bacterial world, Cyanobacteria represents a unique phylogenetic group that is responsible for a key metabolic process in the biosphere - oxygenic photosynthesis - and that includes representatives exhibiting complex morphologies. Many cyanobacteria are multicellular, growing as filaments of cells in which some cells can differentiate to carry out specialized functions. These differentiated cells include resistance and dispersal forms as well as a metabolically specialized form that is devoted to N(2) fixation, known as the heterocyst. In this Review we address cyanobacterial intercellular communication, the supracellular structure of the cyanobacterial filament and the basic principles that govern the process of heterocyst differentiation.
400 citations
Cites background from "Identification of Nostoc punctiform..."
...punctiforme PCC 73102, which is impaired in heterotrophy, akinetes differentiate when the filaments are placed in the dark in the presence of fructos...
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TL;DR: The role of allelopathy in cyanobacteria ecology is still not well understood, and its clarification should benefit from carefully designed field studies, chemical characterization of allelochemicals and new methodological approaches at the “omics” level.
Abstract: Freshwater cyanobacteria produce several bioactive secondary metabolites with diverse chemical structure, which may achieve high concentrations in the aquatic medium when cyanobacterial blooms occur. Some of the compounds released by cyanobacteria have allelopathic properties, influencing the biological processes of other phytoplankton or aquatic plants. These kinds of interactions are more easily detectable under laboratory studies; however their ecological relevance is often debated. Recent research has discovered new allelopathic properties in some cyanobacteria species, new allelochemicals and elucidated some of the allelopathic mechanisms. Ecosystem-level approaches have shed some light on the factors that influence allelopathic interactions, as well as how cyanobacteria may be able to modulate their surrounding environment by means of allelochemical release. Nevertheless, the role of allelopathy in cyanobacteria ecology is still not well understood, and its clarification should benefit from carefully designed field studies, chemical characterization of allelochemicals and new methodological approaches at the "omics" level.
134 citations
Cites background from "Identification of Nostoc punctiform..."
...…error in the outcome of the assay—for discussion on this subject please refer to Bustin (2002) and Ginzinger (2002)—and a survey of the literature reveals that only a few studies which employ this methodology with cyanobacteria have been published (Argueta et al. 2006; Woodger et al. 2003)....
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TL;DR: The differentiation of heterocysts (steady state, N(2) grown), akinetes, and hormogonia appears to involve the up-regulation of genes distinct for each state, consistent with entry into a nongrowth state.
Abstract: The vegetative cells of the filamentous cyanobacterium Nostoc punctiforme can differentiate into three mutually exclusive cell types: nitrogen-fixing heterocysts, spore-like akinetes, and motile hormogomium filaments. A DNA microarray consisting of 6,893 N. punctiforme genes was used to identify the global transcription patterns at single time points in the three developmental states, compared to those in ammonium-grown time zero cultures. Analysis of ammonium-grown cultures yielded a transcriptome of 2,935 genes, which is nearly twice the size of a soluble proteome. The NH4+-grown transcriptome was enriched in genes encoding core metabolic functions. A steady-state N2-grown (heterocyst-containing) culture showed differential transcription of 495 genes, 373 of which were up-regulated. The majority of the up-regulated genes were predicted from studies of heterocyst differentiation and N2 fixation; other genes are candidates for more detailed genetic analysis. Three days into the developmental process, akinetes showed a similar number of differentially expressed genes (497 genes), which were equally up- and down-regulated. The down-regulated genes were enriched in core metabolic functions, consistent with entry into a nongrowth state. There were relatively few adaptive genes up-regulated in 3-day akinetes, and there was little overlap with putative heterocyst developmental genes. There were 1,827 differentially transcribed genes in 24-h hormogonia, which was nearly fivefold greater than the number in akinete-forming or N2-fixing cultures. The majority of the up-regulated adaptive genes were genes encoding proteins for signal transduction and transcriptional regulation, which is characteristic of a motile filament that is poised to sense and respond to the environment. The greatest fraction of the 883 down-regulated genes was involved in core metabolism, also consistent with entry into a nongrowth state. The differentiation of heterocysts (steady state, N2 grown), akinetes, and hormogonia appears to involve the up-regulation of genes distinct for each state.
118 citations
Cites background from "Identification of Nostoc punctiform..."
...NpR4070 was up-regulated in steady-state N2-grown cultures at a significant but low level....
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...and NpR4070) (6) was present in the akinete transcriptome or...
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...Transcription of avaK (NpF5452), encoding an akinete marker protein (6, 48), was enhanced, as was transcription of patA and hetF, whose products are assigned to heterocyst differentiation....
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...None of the four genes determined by differential display to be up-regulated during akinete development (NpF0062, NpF5999, NpF6000, and NpR4070) (6) was present in the akinete transcriptome or in the NH4 -grown transcriptome or proteome....
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...Five genes that are differentially transcribed during akinete differentiation have recently been identified (6, 48)....
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01 Jan 2010
TL;DR: This review focuses on akinetes of Nostocales, emphasizing environmental triggers and cellular responses involved in differentiation, maturation, dormancy, and germination of these resting cells and special attention is given to genetic regulation of the differentiation process.
Abstract: Cyanobacteria are an ancient and morphologically diverse group of photosynthetic prokaryotes, which were the first to evolve oxygenic photosynthesis. Cyanobacteria are widely distributed in diversed environments. In the case of members of the orders Nostocales and Stigonematales, their persistence and success were attributed to their ability to form specialized cells: heterocysts, capable of fixing atmospheric nitrogen and spore-like cells, the akinetes. This review focuses on akinetes of Nostocales, emphasizing environmental triggers and cellular responses involved in differentiation, maturation, dormancy, and germination of these resting cells. Morphological and structural changes, variation in akinete composition, and metabolism are summarized. Special attention is given to the genetic regulation of the differentiation process in an attempt to close gaps in our understanding of the dormancy phenomenon in cyanobacteria and to identify open questions for future research.
100 citations
Cites background or result from "Identification of Nostoc punctiform..."
...These results are consistent with the expression of avaK in A. variabilis (Zhou and Wolk 2002), with N. punctiforme differential display results for aet ( Argueta et al. 2006 ), and with microarray results from zwf akinetes for nblA and avaK (Campbell et al. 2007)....
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...Argueta et al. (2006) reported the detection of three novel genes involved in akinete differentiation....
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TL;DR: The clear differences in the metabolic and morphological adaptations of akinetes of the two species could be related to their different lifestyles and pave the way for genetic and functional studies of akinete differentiation in these species.
Abstract: Akinetes are resting spore-like cells formed by some heterocyst-forming filamentous cyanobacteria for surviving long periods of unfavourable conditions. We studied the development of akinetes in two model strains of cyanobacterial cell differentiation, the planktonic freshwater Anabaena variabilis ATCC 29413 and the terrestrial or symbiotic Nostoc punctiforme ATCC 29133, in response to low light and phosphate starvation. The best trigger of akinete differentiation of Anabaena variabilis was low light; that of N. punctiforme was phosphate starvation. Light and electron microscopy revealed that akinetes of both species differed from vegetative cells by their larger size, different cell morphology and large number of intracellular granules. Anabaena variabilis akinetes had a multilayer envelope; those of N. punctiforme had a simpler envelope. During akinete development of Anabaena variabilis, the amount of the storage compounds cyanophycin and glycogen increased transiently, whereas in N. punctiforme, cyanophycin and lipid droplets increased transiently. Photosynthesis and respiration decreased during akinete differentiation in both species, and remained at a low level in mature akinetes. The clear differences in the metabolic and morphological adaptations of akinetes of the two species could be related to their different lifestyles. The results pave the way for genetic and functional studies of akinete differentiation in these species.
40 citations
Cites background from "Identification of Nostoc punctiform..."
...Here, we showed that low light was the best inducer of akinete formation in Anabaena variabilis and confirmed the earlier finding (Argueta & Summers, 2005; Argueta et al., 2006) that phosphate starvation was the best inducer in N. punctiforme....
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...Here, we showed that low light was the best inducer of akinete formation in Anabaena variabilis and confirmed the earlier finding (Argueta & Summers, 2005; Argueta et al., 2006) that phosphate starvation was the best inducer in N....
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...However, only a few genes involved in akinete formation have been so far identified (e.g. Argueta et al., 2006; Campbell et al., 1996; Leganés et al., 1994, 1998; Lehner et al., 2011; Zhou &Wolk, 2002; see also review by Maldener et al., 2014)....
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References
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TL;DR: A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system.
Abstract: The University of Wisconsin Genetics Computer Group (UWGCG) has been organized to develop computational tools for the analysis and publication of biological sequence data. A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system. The programs available and the conditions for transfer are described.
14,575 citations
"Identification of Nostoc punctiform..." refers methods in this paper
...Sequence features were identified using Wisconsin Genetics Computer Group (GCG) package of programs (Devereux et al., 1984), and BLAST tools available through the National Center for Biotechnology Information (http://www....
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...Sequence features were identified using Wisconsin Genetics Computer Group (GCG) package of programs (Devereux et al., 1984), and BLAST tools available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/)....
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TL;DR: Results are consistent with a function for P-glycoprotein as an energy-dependent efflux pump responsible for decreased drug accumulation in multidrug-resistant cells.
1,914 citations
"Identification of Nostoc punctiform..." refers background in this paper
...NpF0062 protein is also 26% similar and 47% identical over 589 amino acids (E-value 1e-43) to the human multidrug ABC transporter MDR1 (Chen et al., 1986)....
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TL;DR: The Conserved Domain Search service (CD-Search), a web-based tool for the detection of structural and functional domains in protein sequences, uses BLAST(R) heuristics to provide a fast, interactive service, and searches a comprehensive collection of domain models.
Abstract: We describe the Conserved Domain Search service (CD-Search), a web-based tool for the detection of structural and functional domains in protein sequences. CD-Search uses BLAST® heuristics to provide a fast, interactive service, and searches a comprehensive collection of domain models. Search results are displayed as domain architecture cartoons and pairwise alignments between the query and domain-model consensus sequences. Search results may be visualized in further detail by embedding the query sequence into multiple alignment displays and by mapping onto three-dimensional molecular graphic displays of known structures within the domain family. CD-Search can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi.
1,882 citations
"Identification of Nostoc punctiform..." refers background in this paper
...The inferred Aet amino acid sequence is most closely homologous to the COG 1132 group of proteins (Marchler-Bauer and Bryant, 2004) containing multidrug transporters for export of hydrophobic compounds and components of lipopolysaccharides....
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...The second identified gene (NpR4070) was homologous to the beta subunit of a group of heterodimeric proteins comprising the M16 family of zinc-dependent proteases (Marchler-Bauer and Bryant, 2004)....
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Book•
28 Feb 1995
TL;DR: This work focuses on the study of the structure and function of the Photosystem II Reaction Center in Cyanobacteria, which consists of Chloroplast Origins and Evolution, and its role in the Evolution of the Universal Enzyme.
Abstract: Preface. Color Plates. 1. Molecular Evolution and Taxonomy of the Cyanobacteria A. Wilmotte. 2. The Oceanic Cyanobacterial Picoplankton N.G. Carr, N.H. Mann. 3. Prochlorophytes: the 'Other' Cyanobacteria? H.C.P. Matthijs, et al. 4. Molecular Biology of Cyanelles W. Loffelhardt, H.J. Bohnert. 5. Chloroplast Origins and Evolution S.E. Douglas. 6. Supramolecular Membrane Organization E. Gantt. 7. Phycobilisome and Phycobiliprotein Structures W.A. Sidler. 8. The Use of Cyanobacteria in the Study of the Structure and Function of Photosystem II B.A. Barry, et al. 9. The Cytochrome b6f Complex T. Kallas. 10. Photosystem I in Cyanobacteria J.H. Golbeck. 11. The F-type ATPase in Cyanobacteria: Pivotal Point in the Evolution of the Universal Enzyme W.D. Frasch. 12. Soluble Electron Transfer Catalysts of Cyanobacteria L.Z. Morand, et al. 13. Cyanobacterial Respiration G. Schmetterer. 14. The Biochemistry and Molecular Regulation of Carbon Dioxide Metabolism in Cyanobacteria F.R. Tabita. 15. Physiological and Molecular Studies on the Response of Cyanobacteria to Changes in the Ambient Inorganic Carbon Concentration A. Kaplan, et al. 16. Assimilatory Nitrogen Metabolism and its Regulation E. Flores, A. Herrero. 17. Biosynthesis of Cyanobacterial Tetrapyrrole Pigments: Hemes, Chlorophylls, and Phycobilins S.I. Beale. 18. Carotenoids in Cyanobacteria J. Hirschberg, D. Chamovitz. 18. Genetic Analysis of Cyanobacteria T. Thiel. 20. The Transcription Apparatus and the Regulation of Transcription Initiation S.E. Curtis, J.A. Martin. 21. The Responses of Cyanobacteria to Environmental Conditions: Light and Nutrients A.R. Grossman, et al. 22. Short-Term and Long-Term Adaptation of the Photosynthetic Apparatus: Homeostatic Properties of Thylakoids Y. Fujita, et al. 23. Light-Responsive Gene Expression and the Biochemistry of the Photosystem II Reaction Center S.S. Golden. 24. Thioredoxins in Cyanobacteria: Structure and Redox Regulation of Enzyme Activity F.K. Gleason. 25. Iron Deprivation: Physiology and Gene Regulation N.A. Straus. 26. The Cyanobacterial Heat-Shock Response and the Molecular Chaperones R. Webb, L.A. Sherman. 27. Heterocyst Metabolism and Development C.P. Wolk, et al. 28. Differentiation of Hormogonia and Relationships with Other Biological Processes N. Tandeau de Marsac. Organism Index. Gene and Gene Product Index. Subject Index.
1,289 citations
TL;DR: DNA Strider is a new integrated DNA and Protein sequence analysis program written with the C language for the Macintosh Plus, SE and II computers, designed as an easy to learn and use program as well as a fast and efficient tool for the day-to-day sequence analysis work.
Abstract: DNA Strider is a new integrated DNA and Protein sequence analysis program written with the C language for the Macintosh Plus, SE and II computers. It has been designed as an easy to learn and use program as well as a fast and efficient tool for the day-to-day sequence analysis work. The program consists of a multi-window sequence editor and of various DNA and Protein analysis functions. The editor may use 4 different types of sequences (DNA, degenerate DNA, RNA and one-letter coded protein) and can handle simultaneously 6 sequences of any type up to 32.5 kB each. Negative numbering of the bases is allowed for DNA sequences. All classical restriction and translation analysis functions are present and can be performed in any order on any open sequence or part of a sequence. The main feature of the program is that the same analysis function can be repeated several times on different sequences, thus generating multiple windows on the screen. Many graphic capabilities have been incorporated such as graphic restriction map, hydrophobicity profile and the CAI plot- codon adaptation index according to Sharp and Li. The restriction sites search uses a newly designed fast hexamer look-ahead algorithm. Typical runtime for the search of all sites with a library of 130 restriction endonucleases is 1 second per 10,000 bases. The circular graphic restriction map of the pBR322 plasmid can be therefore computed from its sequence and displayed on the Macintosh Plus screen within 2 seconds and its multiline restriction map obtained in a scrolling window within 5 seconds.
984 citations
"Identification of Nostoc punctiform..." refers methods in this paper
...Sequences were manipulated using DNA Strider (Marck, 1988) and BioBike (Massar et al., 2005)....
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...Sequences were manipulated using DNA Strider (Marck, 1988) and BioBike (Massar et al....
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