Evidence for a major role of antisense RNAs in cyanobacterial gene regulation

Information on the numbers and functions of naturally occurring antisense RNAs (asRNAs) in eubacteria has thus far remained incomplete. Here, we screened the model cyanobacterium Synechocystis sp. PCC 6803 for asRNAs using four different methods. In the final data set, the number of known noncoding RNAs rose from 6 earlier identified to 60 and of asRNAs from 1 to 73 (28 were verified using at least three methods). Among these, there are many asRNAs to housekeeping, regulatory or metabolic genes, as well as to genes encoding electron transport proteins. Transferring cultures to high light, carbon-limited conditions or darkness influenced the expression levels of several asRNAs, suggesting their functional relevance. Examples include the asRNA to rpl1, which accumulates in a light-dependent manner and may be required for processing the L11 r-operon and the SyR7 noncoding RNA, which is antisense to the murF 5′ UTR, possibly modulating murein biosynthesis. Extrapolated to the whole genome, ∼10% of all genes in Synechocystis are influenced by asRNAs. Thus, chromosomally encoded asRNAs may have an important function in eubacterial regulatory networks

Fibrisoma limi gen. nov., sp. nov., an orange pigmented filamentous bacterium of the family Cytophagaceae isolated from North Sea tidal flats

An orange pigmented Gram-staining-negative, non motile, filament forming rod-shaped bacterium (BUZ 3T) was isolated from a coastal mud sample from the North Sea (Fedderwardersiel, Germany) and characterized taxonomically using a polyphasic approach. According to 16S rRNA gene sequence data it belongs the family Cytophagaceae, exhibiting low 16S rRNA gene sequence similarity (<90%) to members of the genera Spirosoma, Rudanella and Fibrella. The G+C content was 52.0 mol%. The major fatty acids were summed feature 3 (comprising C16:1{omega}7c and/or isoC15:0 2-OH), C16:1{omega}5c, and isoC17:0 3-OH. The major polar lipids consisted of phosphatidylethanolamine, and several aminolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is proposed that, strain BUZ 3T represents a strain of a novel genus and species, for which the name Fibrisoma limi gen. nov., sp. nov. is proposed. The type strain is BUZ 3T (= DSMZ 22564T = CCUG 58137T

Oxygenic phototrophic biofilms for improved cathode performance in microbial fuel cells

The rate of oxygen reduction reaction in the cathodic chambers of microbial fuel cells (MFCs) is a typical limiting aspect of its performance. Recently, research on biocathodes has gained more interest as it allows circumventing the utilisation of exogenous and unstable mediators at a lower cost. It is shown here that the growth of oxygenic phototrophs as a biofilm, increases the current output by two fold. This was possible by forcing the biofilm to grow onto the cathode, thus, producing the oxygen directly where it was consumed. This enhancement of the cathodic efficiency was stable for over 30. days. © 2013 Elsevier B.V

Subcritical co-solvents extraction of lipid from wet microalgae pastes of Nannochloropsis sp

In this paper subcritical co-solvents extraction (SCE) of algal lipid from wet pastes of Nannochloropsis sp. is examined. The influences of five operating parameters including the ratio between ethanol to hexane, the ratio of mixed solvents to algal biomass (dry weight), extraction temperature, pressure, and time were investigated. The determined optimum extraction conditions were 3:1 (hexane to ethanol ratio), 10:1 ratio (co-solvents to microalgae (dry weight) ratio), 90°C, 1.4 MPa, and 50 min, which could produce 88% recovery rate of the total lipids. In addition, electron micrographs of transmission electron microscopy (TEM) and scanning electron microscopy (SEM) were conducted to show that the algal cell presented shrunken, collapsed with some wrinkles and microholes after SCE extraction. The main composition of total lipids extracted under the optimum conditions was TAG which represented more than 80%. And the fatty acid profile of triglycerides revealed that C16:0 (35.67 ± 0.2%), C18:1 (26.84 ± 0.044%) and C16:1 (25.96 ± 0.011%) were dominant

Origin and evolution of water oxidation before the last common ancestor of the Cyanobacteria

Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster (Mn4CaO5) of Photosystem II. We show that D1 exists in several forms making well-defined clades, some of which could have evolved before the origin of water oxidation and presenting many atypical characteristics. The most ancient form is found in the genome of Gloeobacter kilaueensis JS-1 and this has a C-terminus with a higher sequence identity to D2 than to any other D1. Two other groups of early evolving D1 correspond to those expressed under prolonged far-red illumination and in darkness. These atypical D1 forms are characterized by a dramatically different Mn4CaO5 binding site and a Photosystem II containing such a site may assemble an unconventional metal cluster. The first D1 forms with a full set of ligands to the Mn4CaO5 cluster are grouped with D1 proteins expressed only under low oxygen concentrations and the latest evolving form is the dominant type of D1 found in all cyanobacteria and plastids. In addition, we show that the plastid ancestor had a D1 more similar to those in early branching Synechococcus. We suggest each one of these forms of D1 originated from transitional forms at different stages towards the innovation and optimization of water oxidation before the last common ancestor of all known cyanobacteria

Mutual dependence of the expression of the cell differentiation regulatory protein HetR and the global nitrogen regulator NtcA during heterocyst development

Heterocyst differentiation in the cyanobacterium Anabaena sp. strain PCC 7120 depends on both the global nitrogen regulator NtcA and the cell differentiation regulatory protein HetR, and induction of hetR upon nitrogen step-down depends on NtcA. The use of two out of the four transcription start points (tsps) described for the hetR gene (those located at positions -728 and -271) was found to be dependent on NtcA, and the use of the tsp located at position -271 was also dependent on HetR. Thus, autoregulation of hetR could take place via the activation of transcription from this tsp. Expression of ntcA in nitrogen-fixing cultures was higher than in cells growing in the presence of ammonium or nitrate, and high expression of ntcA under nitrogen deficiency resulted from an increased use of tsps located at positions -180 and -49. The induction of the use of these tsps did not take place in ntcA or hetR mutant strains. These results indicate a mutual dependency in the induction of the regulatory genes hetR and ntcA that takes place in response to nitrogen step-down in Anabaena cells. Expression of the hetC gene, which is also involved in the early steps of heterocyst differentiation, from its NtcA-dependent tsp was, however, not dependent on HetR.Dirección General de Enseñanza Superior e Investigación Científica (PB97-1137)Dirección General de Investigación BMC2001–050

Septal protein SepJ from the heterocyst‐forming cyanobacterium Anabaena forms multimers and interacts with peptidoglycan

Heterocyst‐forming cyanobacteria grow as filaments that can be hundreds of cells long. Proteinaceous septal junctions provide cell–cell binding and communication functions in the filament. In Anabaena sp. strain PCC 7120, the SepJ protein is important for the formation of septal junctions. SepJ consists of integral membrane and extramembrane sections – the latter including linker and coiled‐coil domains. SepJ (predicted MW, 81.3 kDa) solubilized from Anabaena membranes was found in complexes of about 296–334 kDa, suggesting that SepJ forms multimeric complexes. We constructed an Anabaena strain producing a double‐tagged SepJ protein (SepJ‐GFP‐His10) and isolated the tagged protein by a two‐step affinity chromatography procedure. Analysis of the purified protein preparation provided no indication of the presence of specific SepJ partners, but suggested that SepJ is processed to remove an N‐terminal fragment. Additionally, pull‐down experiments showed that His6‐tagged versions of SepJ and of the SepJ coiled‐coil domain interact with Anabaena peptidoglycan (PG). Our results indicate that SepJ forms multimers, that it interacts with PG, and that the coiled‐coil domain is involved in this interaction. These observations support the idea that SepJ is a component of the septal junctions that join the cells in the Anabaena filament

Antagonistic interactions between filamentous heterotrophs and the cyanobacterium Nostoc muscorum

Background: Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria. Here, interactions between the filamentous heterotrophic bacteria Fibrella aestuarina (strain BUZ 2) and Fibrisoma limi (BUZ 3) with an axenic strain of the autotrophic filamentous cyanobacterium Nostoc muscorum (SAG 25.82) were studied in mixed cultures under nutrient rich (carbon source present in medium) and poor (carbon source absent in medium) conditions. Findings: F. aestuarina BUZ 2 significantly reduced the cyanobacterial population whereas F. limi BUZ 3 did not. Physical contact between heterotrophs and autotroph was observed and the cyanobacterial cells showed some level of damage and lysis. Therefore, either contact lysis or entrapment with production of extracellular compounds in close vicinity of host cells could be considered as potential modes of action. The supernatants from pure heterotrophic cultures did not have an effect on Nostoc cultures. However, supernatant from mixed cultures of BUZ 2 and Nostoc had a negative effect on cyanobacterial growth, indicating that the lytic compounds were only produced in the presence of Nostoc. The growth and survival of tested heterotrophs was enhanced by the presence of Nostoc or its metabolites, suggesting that the heterotrophs could utilize the autotrophs and its products as a nutrient source. However, the autotroph could withstand and out-compete the heterotrophs under nutrient poor conditions. Conclusions: Our results suggest that the nutrients in cultivation media, which boost or reduce the number of heterotrophs, were the important factor influencing the outcome of the interplay between filamentous heterotrophs and autotrophs. For better understanding of these interactions, additional research is needed. In particular, it is necessary to elucidate the mode of action for lysis by heterotrophs, and the possible defense mechanisms of the autotrophs

Identification of Substrain-Specific Mutations by Massively Parallel Whole-Genome Resequencing of Synechocystis sp. PCC 6803

The cyanobacterium, Synechocystis sp. PCC 6803, was the first photosynthetic organism whose genome sequence was determined in 1996 (Kazusa strain). It thus plays an important role in basic research on the mechanism, evolution, and molecular genetics of the photosynthetic machinery. There are many substrains or laboratory strains derived from the original Berkeley strain including glucose-tolerant (GT) strains. To establish reliable genomic sequence data of this cyanobacterium, we performed resequencing of the genomes of three substrains (GT-I, PCC-P, and PCC-N) and compared the data obtained with those of the original Kazusa strain stored in the public database. We found that each substrain has sequence differences some of which are likely to reflect specific mutations that may contribute to its altered phenotype. Our resequence data of the PCC substrains along with the proposed corrections/refinements of the sequence data for the Kazusa strain and its derivatives are expected to contribute to investigations of the evolutionary events in the photosynthetic and related systems that have occurred in Synechocystis as well as in other cyanobacteria