Special Issue "Cyanobacteria: Ecology, Physiology and Genetics"

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A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Life Sciences".

Deadline for manuscript submissions: closed (30 October 2014)

Special Issue Editors

Guest Editor
Prof. Dr. Robert Haselkorn
Molecular Genetics & Cell Biology, The University of Chicago, 920 East 58 Street, Chicago IL 60637, USA
Website: https://chemistry.uchicago.edu/faculty/faculty/person/member/robert-haselkorn.html
E-Mail: rh01@uchicago.edu
Interests: cellular differentiation in filamentous cyanobacteria; nitrogen fixation; transcription regulation in cyanobacteria; toxins; genetics

Guest Editor
Prof. Dr. John C. Meeks
Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
Website: http://microbiology.ucdavis.edu/meeks/
E-Mail: jcmeeks@ucdavis.edu
Interests: biology of cyanobacteria; especially cellular differentiation; genome analyses; gliding motility; microbial physiology; nitrogen fixation; photosensors; symbiosis

Special Issue Information

Dear Colleagues,

As oxygen-producing photoautotrophs, cyanobacteria have been, and continue to be, one of the most influential groups of micro-organisms on earth. They are an ancient lineage, with a fossil record dating to at least 3 billion years ago and were singularly responsible for the initial oxygenation of the biosphere. Cyanobacteria are the most nutritionally independent organisms on earth, requiring only light, water, CO2 and a few inorganic molecules or elements for growth; some can fix nitrogen. They areubiquitous in the illuminated portions of the terrestrial and aquatic biosphere, including deep oceanic, hypersaline, geothermal, desert and polar habitats, as well as being endolithic and endophytic. Cyanobacteria display diverse cellular and colonial morphologies, cellular developmental alternatives, types of secondary metabolites, some of which are toxic to metazoans, and behaviors, such as chromatic adaptation, reversible desiccation and genetic adaptation to environmental changes. Molecular genetic evidence is consistent with a common cyanobacterial ancestor giving rise to the chloroplasts of eukaryotic algae and plants. Processes and pathways expressed by extant cyanobacteria, such as circadian rhythms, phytochrome signaling and cellulose synthesis, amongst others, are likely to have entered the plant world via that ancient endosymbiotic event. Many cyanobacteria are amenable to genetic manipulation; therefore, they are excellent experimental systems for studies of photosynthetic and nitrogen metabolism, regulation of the differentiation of specialized cells, cell-cell communication and environmental signal transduction. The genomes of more than 190 cyanobacteria have been sequenced to date and genomic based analyses are being applied to document their changing transcriptome, proteome and metabalome. In this special issue, advanceswill be presented in understanding the ecology, physiology and genetics of cyanobacteria, using classic and molecular genetic approaches that will ultimately aid inmanipulation of selected organisms for biotechnological applications in bioremediation, biofuel and pharmaceutical production.

Prof. Dr. Robert Haselkorn
Prof. Dr. John C. Meeks
Guest Editors

Submission

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Keywords

  • oxygenic photosynthesis
  • nitrogen fixation
  • primary C and N production
  • circadian rhythm
  • toxins and blooms
  • signal transduction
  • photosensors
  • community structure
  • cellular communication
  • cellular differentiation

Published Papers (4 papers)

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Displaying article 1-4
p. 770-787
by , , , , , ,  and
Life 2014, 4(4), 770-787; doi:10.3390/life4040770
Received: 16 August 2014; in revised form: 24 September 2014 / Accepted: 22 October 2014 / Published: 21 November 2014
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(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
p. 745-769
by  and
Life 2014, 4(4), 745-769; doi:10.3390/life4040745
Received: 3 September 2014; in revised form: 31 October 2014 / Accepted: 5 November 2014 / Published: 18 November 2014
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(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
abstract graphic
p. 666-680
by  and
Life 2014, 4(4), 666-680; doi:10.3390/life4040666
Received: 9 September 2014; in revised form: 24 October 2014 / Accepted: 27 October 2014 / Published: 7 November 2014
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(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
p. 433-456
by  and
Life 2014, 4(3), 433-456; doi:10.3390/life4030433
Received: 2 June 2014; in revised form: 9 August 2014 / Accepted: 14 August 2014 / Published: 3 September 2014
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(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type of Paper: Article
Title:
The Interplay between Iron Bioavailability and Transport Strategies in Aquatic Cyanobacteria
Authors:
Hagar Lis 2,3, Chana Kranzler 1,2, Yeala Shaked 2,3 and Nir Keren 1
Affiliations:
1 Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem, Israel
2 Interuniversity Institute for Marine Sciences in Eilat, POB 469, Eilat 88103, Israel
3
The Freddy and Nadine Herrmann Institute of Earth Sciences, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem, Israel
Abstract
: Cyanobacteria are a diverse and highly successful group of organisms, prevalent throughout aquatic ecosystems. Due to their taxonomic affiliation, these photosynthetic prokaryotes are often associated with the siderophore mediated iron uptake strategy employed by heterotrophic bacteria. However, siderophore production is not well suited to dilute heterogeneous ocean environments in which diffusive losses pose significant challenges to this strategy. Moreover, genetic studies show that open ocean cyanobacteria possess neither siderophore biosynthesis nor siderophore transporter genes—capabilities which seem to be limited to freshwater, brackish and coastal environments. Recent studies uncovered an alternative high affinity iron uptake pathway functioning in Fe-limited model cyanobacteria—reduction of Fe(III) species prior to transport though the plasma membrane. In this contribution, we examine the prevalence of this mechanism amongst genetically and ecologically diverse cyanobacterial strains and across several Fe-substrates. Interestingly, we found that siderophore producers are able to acquire iron via the reductive pathway, although implementation of this strategy seems to depend on the chemical nature of the Fe-substrate. Results of short term iron uptake assays also confirm the presence of the reductive strategy in a number of marine species. Thus, reductive iron uptake appears to be a prevalent strategy amongst both fresh water and marine cyanobacteria in the uptake of various Fe-substrates. These findings lend insight into the relationship between environmental pressures and the evolution of cyanobacterial iron uptake strategies.

Type of Paper: Article
Title: Novel DNA Taxonomy Approaches in Cyanobacteria
Author
: Ester Eckert, Diego Fontaneto, Manuela Coci, Gianluca Corno and Cristiana Callieri
Affiliation:
CNR – Institute of Ecosystem Study, Verbania, Italy
Abstract
: Taxonomy in Cyanobacteria is mostly based on 16S sequences, as for all prokaryotes. Nevertheless, the most common approach in DNA taxonomy for cyanobacteria is still based on genetic distances, without incorporating any of the theoretical advances in DNA taxonomy that have been recently developed for eukaryotes. Several methods based on maximum likelihood and Bayesian statistical approaches, also including coalescent theory, have been developed for DNA taxonomy in eukaryotes, but are not yet applied in prokaryotes. Here we demonstrate their reliable and useful application in the case of Cyanobacteria. We test the output of different methods in DNA taxonomy (e.g., ABGD, GMYC, PTP) on 16S sequences of Cyanobacteria cladesand investigate the ecological and physiological independence of the taxonomic units.

Type of Paper: Article
Title:
Control of chromosome copy number depending on growth phase in cyanobacteri
Authors: Satoru Watanabe 1, Ryudo Ohbayashi 1,2, Yu Kanesaki 3, Natsumi Saito 4, Ryuuichi Hirota 5, Naoto Shigenobu 1, Taku Chibazakura 1, Tomoyoshi Soga 4 and Hirofumi Yoshikawa1,2,3,*
Affiliations:
1 Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan; E-Mail: s3watana@nodai.ac.jp (Satoru Watanabe); hiyoshik@nodai.ac.jp (Hirofumi Yoshikawa); Tel.: +81-3-5477-2758 (Hirofumi Yoshikawa); Fax: +81-3-5477-2668 (Hirofumi Yoshikawa)
2
Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
3
Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
4
Laboratory of Genome Designing Biology, Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
5
Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan
Abstract:
While bacteria such as Escherichia coli and Bacillus subtilis harbor a single circular chromosome, some freshwater cyanobacteria have multicopy chromosomes per cell. We have studied the replication and partitioning mechanisms of multicopy chromosomes in cyanobacteria Synechococcus elongatus PCC 7942. In our batch culture condition, the chromosome copy number wassignificantly increased incellsat lag phase, period after releasing from dark in order to synchronize the culture, and it was decreased at bothexponential and stationary phases.Actually, DNA replication activity in lag phase cells was higher than that of exponential and stationary cells. In addition, the lag phase cellswere more sensitive to nalidixic acid, a DNA gyrase inhibitor, than the cells of other phases.In order to investigate cellular physiology of the lag phase in Synechococcus, we compared the gene expression profile and metabolome in each growth phase. As the specific phenomena in the cells at lag phase, 62% of genes were up or down regulated, and the carbon metabolites, amino acids, nucleotidesand polyphosphates were accumulated. These results suggested that the Synechococcus cells at lag phase already start replicating and prepare chromosome and metabolites for division and elongation at the following phases.

Type of Paper: Article
Title
: The Effects of Dark Incubation on Cellular Metabolism of the Wild Type and the Mutant Lacking the Transcriptional Regulator cyAbrB2 in the Cyanobacterium Synechocystis sp. PCC 6803
Authors
: Masamitsu Hanai 1, Yusuke Sato 1, Atsuko Miyagi 1, Maki Kawai-Yamada 1,2, Kyoko Tanaka 1, Yasuko Kaneko 1,2, Yoshitaka Nishiyama 1,2 and Yukako Hihara 1,2,3
Affiliations:
1 Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
2
Institute for Environmental Science and Technology, Saitama University, Saitama 338-8570, Japan
3
PRESTO, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
Abstract:
In the cyanobacterium Synechocystis sp. PCC 6803 grown under light conditions, the cyAbrB2 transcriptional regulator has been shown to play a key role in regulating cellular metabolism. In this study, we examined the role of cyAbrB2 in metabolic regulation under dark conditions by characterizing the wild type (WT) and the cyabrB2-disrupted mutant cells using a metabolomic approach. Glycogen, glucose-1-phosphate and sugar phosphates located at the upper portion of glycolysis were highly accumulated, whereas amounts of 3-phosphoglycerate, phosphoenolpyruvate and ribulose 1,5-bisphosphate were significantly lower in the mutant under light conditions. Such differences in metabolite levels between WT and the mutant became less conspicuous during dark incubation due to the general decrease of metabolites. Notable exceptions were increase in 2-oxoglutarate, histidine, ornithine and citrulline observed in the dark-incubated WT but not in the mutant. Highly accumulated glycogen granules in the mutant cells under light conditions could be actively metabolized to drive respiration under dark conditions. These results together with the observation of the marked decrease of cyAbrBs in dark both in transcript and protein levels suggest that cyAbrB2 plays only a minor role during dark period. When grown under light-dark cycle conditions, glycogen content of the mutant was normally decreased in the first dark period. However, the rate of decrease was significantly lower in the second dark period and diurnal oscillatory pattern of glycogen content was lost afterward, indicating that cyAbrB2 is required for the proper switching between day and night metabolisms.

Title: Advances in understanding carboxysome assembly in Prochlorococcus and Synechococcus.
Authors:
Fei Cai 1,2, Sabine Heinhorst 3, Gordon C. Cannon 3 and Cheryl A. Kerfeld1,2,4,*
Affiliations:
1 Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
2
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
3
Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-5043, USA
4
MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
Abstract
: The Marine Synechococcus and Prochlorococcus are numerically dominant cyanobacteria in the open ocean. They have evolved a CO2-concentrating-mechanism (CCM) to improve photosynthetic performance, and therefore play an important role in global carbon fixation. Carboxysomes, the central component of the CCM, are self-assembling proteinaceous organelles. Two types of carboxysome, α and β, encapsulating the form IA and form IB D-ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) respectively, differ in gene organization and associated proteins. Relative to the β-carboxysome, the assembly process of the α-carboxysome is enigmatic. A large (>760 amino acids) protein, CsoS2, has no counterpart in the β-carboxysomes and appears to play an essential role in the formation and function of α-carboxysomes. Biochemical, genetic, and structural studies revealed that it is vital for α-carboxysome biogenesis. The primary structure of CsoS2 is distinctive and appears to be composed of three domains: N-terminal, Middle (M)-, and C-terminal domains. Repetitive motifs can be identified in N- and M-domain, respectively. This protein has proven recalcitrant to crystallization and multiple lines of evidence suggested CsoS2 is highly flexible. In this study, we took bioinformatic, biophysical, genetic, biochemical approaches, including peptide array scanning for protein-protein interaction discovery, to understand the role of CsoS2 in the structure, function and assembly of the α-carboxysome.

Title: Chlorophyll biosynthesis of cyanobacteria under low oxygen environments and evolutionary implications
Authors:
Rina Aoki, Ryoma Tsujimoto and Yuichi Fujita
Affiliations:
Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
Abstract:
Chlorophyll a (Chl), the tetrapyrrole pigment essential for photosynthesis, is produced from glutamate via a complex biosynthetic pathway consisting of at least 15 enzymatic steps. Former half is shared with heme biosynthesis and latter half is specific to Chl a so-called Mg-branch. In addition, bilin pigments such as phycocyanobilin are produced from heme. Some steps in the biosynthetic pathways of Chl and bilins require molecular oxygen (O2) for catalysis such as oxygen-dependent coproporphyrinogen III oxidase. Cyanobacteria thrive in diverse environments in terms of oxygen levels. To cope with Chl deficiency caused by low oxygen conditions, cyanobacteria develop elaborate mechanisms to maintain Chl production even under micro-oxic environments. Use of enzymes specialized for low oxygen conditions such as oxygen-independent coproporphyrinogen III oxidase constitutes a part of the mechanisms. Another layer of the mechanisms is mediated by a transcriptional regulator called ChlR that senses low oxygen to activate the transcription of genes encoding low-oxygen type enzymes. In diazotrophic cyanobacteria this multilayered regulation also contributes in Chl biosynthesis to support energy production for nitrogen fixation that requires low oxygen conditions. Low-oxygen type enzymes appear to be evolutionary older than oxygen-dependent enzymes. We will also discuss evolutionary implications of cyanobacterial Chl biosynthesis and regulation.

Title: Regulation of Three Nitrogenase Gene Clusters in the Cyanobacterium Anabaena variabilis ATCC 29413
Authors:
Teresa Thiel and Brenda S. Pratte
Affiliation:
Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA
Abstract:
The filamentous cyanobacterium Anabaena variabilis ATCC 29413 fixes nitrogen under aerobic conditions in specialized cells called heterocysts that form in response to an environment deficient in combined nitrogen. Nitrogen fixation is mediated by the enzyme nitrogenase, which is very sensitive to oxygen. Heterocysts are microxic cells that allow nitrogenase to function in a filament comprised primarily of vegetative cells that produce oxygen by photosynthesis. A. variabilis is unique among well-characterized cyanobacteria in that it has three nitrogenase gene clusters that encode different nitrogenases, which function under different environmental conditions. The nif1 genes encode a Mo-nitrogenase that functions only in heterocysts, even in filaments grown anaerobically. The nif2 genes encode a different Mo-nitrogenase that functions in vegetative cells and heterocysts, but only in filaments grown under anoxic conditions. An alternative V-nitrogenase is encoded by vnf genes that are expressed only in heterocysts in an environment that is deficient in Mo. Thus, these three nitrogenases are expressed differentially in response to environmental conditions. The multi-gene nif1 and nif2clusters show strong similarity in gene organization, while the vnf genes show a different organization. The entire nif1 gene cluster, comprising at least 15 genes, is primarily under the control of the promoter for the first gene, nifB1. Transcriptional control of many of the downstream nif1 genes occurs by a combination of weak promoters within the coding regions of some downstream genes and by RNA processing, which is associated with increased transcript stability. The vnf genes show a similar pattern of transcriptional and post-transcriptional control of expression suggesting that the complex pattern of regulation of the nif1 cluster is conserved in other cyanobacterial nitrogenase gene clusters.

Type of Paper: Article
Title:
Diminished Light Harvesting Capability Effects Photosystem Function in the Cyanobacterium Synechocystis sp. PCC 6803
Authors:
Aparna Nagarajan 1, Lawrence E. Page 1,2, Michelle Liberton 1 and Himadri B. Pakrasi 1,*
Affiliations:
1 Department of Biology, Washington University, St. Louis, MO 63130, USA
2
Current address: Terra Biologics, St. Louis, MO 6313
Abstract: Cyanobacteria use phycobilisomes,large pigment-protein complexes, to harvest light energy primarily for photosystem II (PSII). We have used a series of mutants with partial to complete reduction of phycobilisomes to examine the effects of antenna truncation on photosystem function in Synechocystis sp. PCC 6803. Our results showed that the antenna mutants CB, CK, and PAL express increasing levels of functional PSII to compensate for the loss of phycobilisomes, with a concomitant decrease in PSI. This increased PSII titer leads to progressively higher oxygen evolution rates on a per chlorophyll basis, while at the same time these mutants demonstrate difficulty in S-state transitions. Thus, a decrease in antenna size leads to physiological changes in light harvesting and energy transfer to PSII that result in detrimental effects on photoautotrophic productivity in this cyanobacterium.

Article type: Review
Title:
Sucrose in Cyanobacteria: From a Salt-Response Molecule to a Key role in Nitrogen-Fixation
Authors:
Graciela L. Salerno *, María A. Kolman, Macarena Perez-Cenci, Carolina Nishi
Affiliation
: Instiuto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Argentina
Abstract:
In the biosphere, sucrose is synthesized mainly in oxygenic photosynthetic organisms as part of the carbon dioxide assimilation pathway. Its central role in the functional biology of vascular plants is well documented. However, much less is known about the function of sucrose in cyanobacteria, prokaryotes that perform photosynthesis as plants do. Traditionally, sucrose accumulation has been associated with salinity, and, consequently, the disaccharide has been considered as a compatible solute in numerous strains. Also, sucrose has been proposed as the carbon transport molecule in the diazotrophic filaments of heterocyst-forming cyanobacteria. However this has not yet been fully demonstrated. In the last years, functional characterizations of sucrose metabolizing enzymes, metabolic control analysis, cellular localization of encoding gene expression, and reverse genetic experiments, revealed that sucrose metabolism is coordinated with glycogen synthesis and it is crucial in diazotrophic growth. The analysis of more than 20 fully sequenced genomes gave us new insights about the origin of sucrose metabolism and further evolution in the cyanobacterial lineage.

Article type: Review
Title:
Cyanobacteria as Chassis for Industrial Biotechnology: Progress and Prospects
Authors:
Lamya Al-Haj 1, Yuen Tin Lui 2 and Saul Purton 2,*
Affiliations:
1 Sultan Qaboos University, Muscat, Sultanate of Oman
2
Institute of Structural & Molecular Biology, University College London, London WC1E 6BT, UK
Abstract:
Cyanobacteriahold significant potential as industrial biotechnology (IB) platforms for the production of a wide variety of bio-products ranging from biofuel molecules such as hydrogen, alcohols and isoprenoids, to high-value bioactives and recombinant proteins. Underpinning this are recent advances in cyanobacterial omics research, the development of improved genetic engineering tools for key species, and the emerging field of cyanobacterial synthetic biology. Such technologies are now making possible elaborate metabolic engineering programs aimed at creating designer strains tailored for different IB applications. In this review, we provide an overview of the current status of the field with specific focus on the molecular tools and technologies, and we consider future commercial applications.

Last update: 6 October 2014

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