Integration of plastids with their hosts: Lessons learned from dinoflagellates.

After their endosymbiotic acquisition, plastids become intimately connected with the biology of their host. For example, genes essential for plastid function may be relocated from the genomes of plastids to the host nucleus, and pathways may evolve within the host to support the plastid. In this review, we consider the different degrees of integration observed in dinoflagellates and their associated plastids, which have been acquired through multiple different endosymbiotic events. Most dinoflagellate species possess plastids that contain the pigment peridinin and show extreme reduction and integration with the host biology. In some species, these plastids have been replaced through serial endosymbiosis with plastids derived from a different phylogenetic derivation, of which some have become intimately connected with the biology of the host whereas others have not. We discuss in particular the evolution of the fucoxanthin-containing dinoflagellates, which have adapted pathways retained from the ancestral peridinin plastid symbiosis for transcript processing in their current, serially acquired plastids. Finally, we consider why such a diversity of different degrees of integration between host and plastid is observed in different dinoflagellates and how dinoflagellates may thus inform our broader understanding of plastid evolution and function.This is the author accepted manuscript. The final version is available from PNAS via http://dx.doi.org/10.1073/pnas.142138011

Diversity of transcripts and transcript processing forms in plastids of the dinoflagellate alga Karenia mikimotoi.

Plastids produce a vast diversity of transcripts. These include mature transcripts containing coding sequences, and their processing precursors, as well as transcripts that lack direct coding functions, such as antisense transcripts. Although plastid transcriptomes have been characterised for many plant species, less is known about the transcripts produced in other plastid lineages. We characterised the transcripts produced in the fucoxanthin-containing plastids of the dinoflagellate alga Karenia mikimotoi. This plastid lineage, acquired through tertiary endosymbiosis, utilises transcript processing pathways that are very different from those found in plants and green algae, including 3' poly(U) tail addition, and extensive substitutional editing of transcript sequences. We have sequenced the plastid transcriptome of K. mikimotoi, and have detected evidence for divergent evolution of fucoxanthin plastid genomes. We have additionally characterised polycistronic and monocistronic transcripts from two plastid loci, psbD-tRNA (Met)-ycf4 and rpl36-rps13-rps11. We find evidence for a range of transcripts produced from each locus that differ in terms of editing state, 5' end cleavage position, and poly(U) tail addition. Finally, we identify antisense transcripts in K. mikimotoi, which appear to undergo different processing events from the corresponding sense transcripts. Overall, our study provides insights into the diversity of transcripts and processing intermediates found in plastid lineages across the eukaryotes.This work was supported by a BBSRC doctoral training grant [BB/F017464/1, to RGD], and a British Phycological Society summer undergraduate studentship [to GAH].This is the final version of the article. It was first available from Springer via http://dx.doi.org/10.1007/s11103-015-0408-

Cytochrome cM decreases photosynthesis under photomixotrophy in Synechocystis sp. PCC 6803

Photomixotrophy is a metabolic state that enables photosynthetic microorganisms to simultaneously perform photosynthesis and metabolism of imported organic carbon substrates. This process is complicated in cyanobacteria, since many, including Synechocystis sp. PCC 6803, conduct photosynthesis and respiration in an interlinked thylakoid membrane electron transport chain. Under photomixotrophy, the cell must therefore tightly regulate electron fluxes from photosynthetic and respiratory complexes. In this study, we demonstrate, via characterization of photosynthetic apparatus and the proteome, that photomixotrophic growth results in a gradual inhibition of QA- reoxidation in wild-type Synechocystis, which largely decreases photosynthesis over 3 d of growth. This process is circumvented by deleting the gene encoding cytochrome cM (CytM), a cryptic c-type heme protein widespread in cyanobacteria. The ΔCytM strain maintained active photosynthesis over the 3-d period, demonstrated by high photosynthetic O2 and CO2 fluxes and effective yields of PSI and PSII. Overall, this resulted in a higher growth rate compared to that of the wild type, which was maintained by accumulation of proteins involved in phosphate and metal uptake, and cofactor biosynthetic enzymes. While the exact role of CytM has not been determined, a mutant deficient in the thylakoid-localized respiratory terminal oxidases and CytM (ΔCox/Cyd/CytM) displayed a phenotype similar to that of ΔCytM under photomixotrophy. This, in combination with other physiological data, and in contrast to a previous hypothesis, suggests that CytM does not transfer electrons to these complexes. In summary, our data suggest that CytM may have a regulatory role in photomixotrophy by modulating the photosynthetic capacity of cells

Photosynthetic, respiratory and extracellular electron transport pathways in cyanobacteria.

Cyanobacteria have evolved elaborate electron transport pathways to carry out photosynthesis and respiration, and to dissipate excess energy in order to limit cellular damage. Our understanding of the complexity of these systems and their role in allowing cyanobacteria to cope with varying environmental conditions is rapidly improving, but many questions remain. We summarize current knowledge of cyanobacterial electron transport pathways, including the possible roles of alternative pathways in photoprotection. We describe extracellular electron transport, which is as yet poorly understood. Biological photovoltaic devices, which measure electron output from cells, and which have been proposed as possible means of renewable energy generation, may be valuable tools in understanding cyanobacterial electron transfer pathways, and enhanced understanding of electron transfer may allow improvements in the efficiency of power output. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.We are grateful to the Environmental Services Association Education Trust, EnAlgae (European Regional Development Fund: INTERREG IVB NEW programme), and the Department of Biotechnology, India, for financial support.This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.bbabio.2015.10.00

The Chloroplast Genome of a Symbiodinium sp. Clade C3 Isolate

Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as ‘minicircles’. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any ‘empty’ minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic

Identification of Sequences Encoding Symbiodinium minutum Mitochondrial Proteins.

The dinoflagellates are an extremely diverse group of algae closely related to the Apicomplexa and the ciliates. Much work has previously been undertaken to determine the presence of various biochemical pathways within dinoflagellate mitochondria. However, these studies were unable to identify several key transcripts including those encoding proteins involved in the pyruvate dehydrogenase complex, iron-sulfur cluster biosynthesis, and protein import. Here, we analyze the draft nuclear genome of the dinoflagellate Symbiodinium minutum, as well as RNAseq data to identify nuclear genes encoding mitochondrial proteins. The results confirm the presence of a complete tricarboxylic acid cycle in the dinoflagellates. Results also demonstrate the difficulties in using the genome sequence for the identification of genes due to the large number of introns, but show that it is highly useful for the determination of gene duplication events.We would like to thank Richard Dorrell (University of Cambridge) and Ross Waller (University of Cambridge) for useful discussions. This work was supported by a Wellcome Trust Project Grant [WT094249] to CJH and RERN; and an Australian Postgraduate Award to ERB.This is the final version of the article. It first appeared from Oxford University Press via https://doi.org/10.1093/gbe/evw00

An Engineered Community Approach for Industrial Cultivation of Microalgae.

Although no species lives in isolation in nature, efforts to grow organisms for use in biotechnology have generally focused on a single-species approach, particularly where a product is required at high purity. In such scenarios, preventing the establishment of contaminants requires considerable effort that is economically justified. However, for some applications in biotechnology where the focus is on lower-margin biofuel production, axenic culture is not necessary, provided yields of the desired strain are unaffected by contaminants. In this article, we review what is known about interspecific interactions of natural algal communities, the dynamics of which are likely to parallel contamination in industrial systems. Furthermore, we discuss the opportunities to improve both yields and the stability of cultures by growing algae in multi-species consortia.EK acknowledges funding from the FP7 DEMA project (Reference number 309086). ASR received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013/ under REA grant agreement n° 317184.This is the accepted manuscript. This is a copy of an article published in Industrial Biotechnology © 2014 [copyright Mary Ann Liebert, Inc.]; Industrial Biotechnology is available online at: http://online.liebertpub.com

Porous translucent electrodes enhance current generation from photosynthetic biofilms.

Some photosynthetically active bacteria transfer electrons across their membranes, generating electrical photocurrents in biofilms. Devices harvesting solar energy by this mechanism are currently limited by the charge transfer to the electrode. Here, we report the enhancement of bioelectrochemical photocurrent harvesting using electrodes with porosities on the nanometre and micrometre length scale. For the cyanobacteria Nostoc punctiforme and Synechocystis sp. PCC6803 on structured indium-tin-oxide electrodes, an increase in current generation by two orders of magnitude is observed compared to a non-porous electrode. In addition, the photo response is substantially faster compared to non-porous anodes. Electrodes with large enough mesopores for the cells to inhabit show only a small advantage over purely nanoporous electrode morphologies, suggesting the prevalence of a redox shuttle mechanism in the electron transfer from the bacteria to the electrode over a direct conduction mechanism. Our results highlight the importance of electrode nanoporosity in the design of electrochemical bio-interfaces

Evolution of Chloroplast Transcript Processing in Plasmodium and Its Chromerid Algal Relatives

Chloroplasts contain their own genomes, containing two broad functional types of gene: genes encoding proteins directly involved in photosynthesis, and genes with a non-photosynthesis function, such as cofactor biosynthesis, assembly of protein complexes, or expression of the chloroplast genome. Thus far, to our knowledge, no chloroplast gene expression pathways in any lineage have been found to target one functional category of gene specifically. Here, we show that a chloroplast RNA processing pathway – the addition of a 3′ poly(U) tail – is specifically associated with photosynthesis genes in two species of algae, the ‘chromerids’ Chromera and Vitrella. The addition of the poly(U) tail enables the precise processing of mature photosynthesis gene transcripts from precursor RNA, and is likely to be essential for expression of the chromerid photosynthesis machinery. The chromerid algae are the closest photosynthetic relatives of a parasitic group of eukaryotes, the apicomplexans, which include the malaria pathogen Plasmodium. Apicomplexans are descended from algae, and retain a reduced chloroplast, which contains genes only of non-photosynthesis function. We have confirmed that 3′ poly(U) tails are not added to Plasmodium chloroplast transcripts. The expression pathways associated with photosynthesis genes have therefore been lost in the evolution of the apicomplexan chloroplast, and this loss could potentially have driven the transition from photosynthesis to parasitism