Phylogenetic Analysis of Sulfate Assimilation and Cysteine Biosynthesis in Phototrophic Organisms

Patron, Nicola J.; Keeling, Patrick J.; Leustek, Thomas

doi:10.1007/978-1-4020-6863-8_3

Cited by 18 publications

(9 citation statements)

References 137 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Further differences in amino acid production include the production of cysteine and methionine. While sulfate assimilation is essential for phototrophic growth to produce cysteine and methionine, it is usually absent in organisms that ingest sulfur containing cysteine and methionine (Kopriva et al, 2008). Therefore, heterotrophic chrysophytes should be able to obtain reduced sulfur compounds from ingested prey.…”

Section: Resultsmentioning

confidence: 99%

Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes

Beißer

Graupner

Böck

et al. 2017

PeerJ

View full text Add to dashboard Cite

BackgroundChrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes.ResultsWe sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae.ConclusionsOur study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.

show abstract

Section: Resultsmentioning

confidence: 99%

Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes

Beißer

Graupner

Böck

et al. 2017

PeerJ

View full text Add to dashboard Cite

show abstract

“…Nevertheless and contrary to the misleading nomenclature, many of these bacteria are also able to use sulfur compounds as a source of electrons (Imhoff et al 2005). It is now well established that a number of purple non-sulfur bacteria are able to grow photolithoautotrophically with reduced sulfur compounds such as Rhodobacter , Rhodopseudomonas , Rhodoferax , and Rubrivivax , which can use hydrogen, sulfide, thiosulfate, or ferrous iron as electron donors to support their anoxic, phototrophic growth (Kopriva et al 2008). …”

Section: Discussionmentioning

confidence: 99%

Sulfur bacteria in wastewater stabilization ponds periodically affected by the ‘red-water’ phenomenon

Belila

Abbas

Fazaa

et al. 2012

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

Several wastewater stabilization ponds (WSP) in Tunisia suffer periodically from the ‘red-water’ phenomenon due to blooming of purple sulfur bacteria, indicating that sulfur cycle is one of the main element cycles in these ponds. In this study, we investigated the microbial diversity of the El Menzeh WSP and focused in particular on the different functional groups of sulfur bacteria. For this purpose, we used denaturing gradient gel electrophoresis of PCR-amplified fragments of the 16S rRNA gene and of different functional genes involved in microbial sulfur metabolism (dsrB, aprA, and pufM). Analyses of the 16S rRNA revealed a relatively high microbial diversity where Proteobacteria, Chlorobi, Bacteroidetes, and Cyanobacteria constitute the major bacterial groups. The dsrB and aprA gene analysis revealed the presence of deltaproteobacterial sulfate-reducing bacteria (i.e., Desulfobacter and Desulfobulbus), while the analysis of 16S rRNA, aprA, and pufM genes assigned the sulfur-oxidizing bacteria community to the photosynthetic representatives belonging to the Chlorobi (green sulfur bacteria) and the Proteobacteria (purple sulfur and non sulfur bacteria) phyla. These results point on the diversity of the metabolic processes within this wastewater plant and/or the availability of sulfate and diverse electron donors.Electronic supplementary materialThe online version of this article (doi:10.1007/s00253-012-3931-5) contains supplementary material, which is available to authorized users.

show abstract

“…Reliability for internal branch was assessed using the aLRT test and is presented on the graph. Number next to species name represents entry code of given protein in a databank Sulfur assimilation in Thalassiosira pseudonana organism is able to reduce APS with 100-fold higher activity than respective isoforms in plants (Gao et al 2000;Kopriva et al 2008). In our investigation, the phylogenetic tree was reconstructed using both APS and PAPS reductase sequences from other organisms.…”

Section: Phylogenetic Analysis Of Sulfate Transporters/permeasesmentioning

confidence: 99%

Phylogenetic aspects of the sulfate assimilation genes from Thalassiosira pseudonana

2013

View full text Add to dashboard Cite

Diatoms are unicellular algae responsible for approximately 20 % of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids. In the last years the interest on unicellular algae increased. On the one hand assessments suggest that diatom-mediated export production can influence climate change through uptake and sequestration of atmospheric CO2. On the other hand diatoms are in focus because they are discussed as potential producer of biofuels. To follow the one or other idea it is necessary to investigate the diatoms biochemistry in order to understand the cellular regulatory mechanisms. The sulfur assimilation and methionine synthesis pathways provide S-containing amino acids for the synthesis of proteins and a range of metabolites such as dimethylsulfoniopropionate (DMSP) in order to provide basic metabolic precursors needed for the diatoms metabolism. To obtain an insight into the localization and organization of the sulfur metabolism pathways, the genome of Thalassiosira pseudonana-a model organism for diatom research-might help to understand the fundamental questions on adaptive responses of diatoms to dynamic environmental conditions such as nutrient availability in a broader context.

show abstract

Phylogenetic Analysis of Sulfate Assimilation and Cysteine Biosynthesis in Phototrophic Organisms

Cited by 18 publications

References 137 publications

Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes

Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes

Sulfur bacteria in wastewater stabilization ponds periodically affected by the ‘red-water’ phenomenon

Phylogenetic aspects of the sulfate assimilation genes from Thalassiosira pseudonana

Contact Info

Product

Resources

About