Summary Symbiotic animals containing green photobionts challenge the common perception that only ... more Summary Symbiotic animals containing green photobionts challenge the common perception that only plants are capable of capturing the sun's rays and converting them into biological energy through photoautotrophic CO2 fixation (photosynthesis). ‘Solar-powered’ sacoglossan molluscs, or sea slugs, have taken this type of symbiotic association one step further by solely harboring the photosynthetic organelle, the plastid (=chloroplast). One such sea slug, Elysia chlorotica, lives as a ‘plant’ when provided with only light and air as a result of acquiring plastids during feeding on its algal prey Vaucheria litorea. The captured plastids (kleptoplasts) are retained intracellularly in cells lining the digestive diverticula of the sea slug, a phenomenon sometimes referred to as kleptoplasty. Photosynthesis by the plastids provides E. chlorotica with energy and fixed carbon for its entire lifespan of ∼10 months. The plastids are not transmitted vertically (i.e. are absent in eggs) and do ...
Experimental Materials Nor and Tnd standards of purity 101.08Ϯ0.85 (w/w) and 100.57Ϯ0.87 (w/w) re... more Experimental Materials Nor and Tnd standards of purity 101.08Ϯ0.85 (w/w) and 100.57Ϯ0.87 (w/w) respectively, according to European Pharmacopoeia 2005 methods, were kindly supplied by Pharaonia Pharmaceuticals (for Wockhardt, Egypt). Conaz ® tablets of batches 16929 and 16932 labeled to contain 400 mg Nor and 600 mg Tnd/tablet were from Pharaonia Pharmaceuticals (for Wockhardt, Egypt). Apparatus and Reagents A Shimadzu Ultraviolet/Visible spectrophotometer 1601-pc (Tokyo, Japan) with matched 1 cm quartz cells and connected to IBM compatible computer was used. Shimadzu-Dual wavelength lamp flying CS-9301 densitometer and ultraviolet short wavelength lamp (254 nm) were used. HPTLC plates were silica gel/TLC cards with fluorescent indicator (254 nm); layer thickness 0.2 mm; 20ϫ20 cm aluminum cards (Fluka). HPLC instrument was Hewlett Packard series 1100 equipped with a quaternary pump, diode array detector and a manual injector 20 ml loop (Minnesota, U.S.A.). Detection was carried at 280 nm and flow rate was 1 ml/min. Column used was m-Bondapack C18, 5 mm (300ϫ3.9 mm I.D.) was from Waters (Milford, U.S.A.). Ultrasonic was J.P. Selecta, s-a, CD. 300513, Spain. Methanol and acetonitrile (HPLC and Analytical grades) were from Lab scan Analytical Sciences (New Jersey, U.S.A.). Buffer used in mobile phase for LC method was 0.1 M sodium dihydrogen phosphate (Merck, Darmstadt, Germany) containing 0.005 M pentane sulfonic acid sodium salt and adjusted to pH 3.2 with phosphoric acid. Isopropanol and nbutanol were obtained from Lab scan analytical sciences (New Jersey, U.S.A.), pentane sulphonic acid was obtained from Acros organics (Geel, Belgium), phosphoric acid and concentrated ammonia were obtained from Riedel de-Haen (St. Louis, Missouri, U.S.A.). Preparation of Decarboxylated Nor Decarboxylated Nor was prepared according to the method reported by S. Z. El-Khateeb et al., 15) where the decarboxylated Nor was separated and collected from preparative TLC glass plates using the mobile phase applied in the TLC-densitometric method. The scratched degradant was dissolved in methanol and filtered. The filtrate was evaporated to dryness and the residue was collected. Stock Solutions Four stock solutions were prepared: Stock solution 1: 50 mg Nor was transferred into a 50-ml volumetric flask, dissolved in 2 ml
Under the endosymbiont hypothesis, over a billion years ago a heterotrophic eukaryote entered int... more Under the endosymbiont hypothesis, over a billion years ago a heterotrophic eukaryote entered into a symbiotic relationship with a cyanobacterium (the cyanobiont). This partnership culminated in the plastid that has spread to forms as diverse as plants and diatoms. However, why primary plastid acquisition has not been repeated multiple times remains unclear. Here, we report a possible answer to this question by showing that primary plastid endosymbiosis was likely to have been primed by the secretion in the host cytosol of effector proteins from intracellular Chlamydiales pathogens. We provide evidence suggesting that the cyanobiont might have rescued its afflicted host by feeding photosynthetic carbon into a chlamydia-controlled assimilation pathway.
There is great body of evidence showing a relationship between childhood adversity and psychosis ... more There is great body of evidence showing a relationship between childhood adversity and psychosis onset. Genetic factors moderate the association between childhood adversity and psychosis risk potentially by influencing biological and/or psychological reaction following exposure to adversity. In this review, we discuss studies identifying the specific genetic variants known to affect dopamine levels involved in this interaction. Our review shows that the catechol-O-methyltransferase (COMT), dopamine D2 receptor (DRD2), AKT1 gene play a key role in mediating the relationship between childhood adversity and development of psychosis. We have also found conflicting findings on the impact of dopamine genes on the relationship between childhood adversity and development of psychosis, suggesting that other genetic and environmental factors should be taken into account. We here discuss the implications of our findings and future directions.
Red seaweeds are key components of coastal ecosystems and are economically important as food and ... more Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.
My dissertation focuses on genome and functional evolution of photosynthetic eukaryotes and the d... more My dissertation focuses on genome and functional evolution of photosynthetic eukaryotes and the design and implementation of computational methods and tools to enable genome-wide studies to investigate these taxa.
Phylogenomics, conventionally defined as the intersection of phylogenetics and genomics, has beco... more Phylogenomics, conventionally defined as the intersection of phylogenetics and genomics, has become a key instrument in a wide spectrum of biological studies, including resolution of complex evolutionary relationships, assignment of taxonomic affiliation, prediction of protein molecular functions, and tracing horizontal gene transfer event. Here, we introduce an open-source phylogenomic pipeline, iTree, which automates the execution of phylogenetic analyses under multithreaded and grid-computing environments, providing a scalable high-throughput platform for performing genome-wide evolutionary analyses. Furthermore, we describe the results of two applications of using iTree: (1) taxonomic assignment of 16S ribosomal RNA sequences from human oral metagenomic samples and (2) detection of horizontal gene transfer in microbial genomes.
The seafloor is a unique environment, which allows insights into how geochemical processes affect... more The seafloor is a unique environment, which allows insights into how geochemical processes affect the diversity of biological life. Among its diverse ecosystems are deep-sea brine pools -water bodies characterized by a unique combination of extreme conditions. The 'polyextremophiles' that constitute the microbial assemblage of these deep hot brines have not been comprehensively studied. We report a comparative taxonomic analysis of the prokaryotic communities of the sediments directly below the Red Sea brine pools, namely, Atlantis II, Discovery, Chain Deep, and an adjacent brine-influenced site. Analyses of sediment samples and high-throughput pyrosequencing of PCR-amplified environmental 16S ribosomal RNA genes (16S rDNA) revealed that one sulfur (S)-rich Atlantis II and one nitrogen (N)-rich Discovery Deep section contained distinct microbial populations that differed from those found in the other sediment samples examined. Proteobacteria, Actinobacteria, Cyanobacteria, Deferribacteres, and Euryarchaeota were the most abundant bacterial and archaeal phyla in both the S-and N-rich sections. Relative abundance-based hierarchical clustering of the 16S rDNA pyrotags assigned to major taxonomic groups allowed us to categorize the archaeal and bacterial communities into three major and distinct groups; group I was unique to the S-rich Atlantis II section (ATII-1), group II was characteristic for the N-rich Discovery sample (DD-1), and group III reflected the composition of the remaining sediments. Many of the groups detected in the S-rich Atlantis II section are likely to play a dominant role in the cycling of methane and sulfur due to their phylogenetic affiliations with bacteria and archaea involved in anaerobic methane oxidation and sulfate reduction.
Proceedings of The National Academy of Sciences, 2008
The sea slug Elysia chlorotica acquires plastids by ingestion of its algal food source Vaucheria ... more The sea slug Elysia chlorotica acquires plastids by ingestion of its algal food source Vaucheria litorea. Organelles are sequestered in the mollusc's digestive epithelium, where they photosynthesize for months in the absence of algal nucleocytoplasm. This is perplexing because plastid metabolism depends on the nuclear genome for >90% of the needed proteins. Two possible explanations for the persistence of photosynthesis in the sea slug are (i) the ability of V. litorea plastids to retain genetic autonomy and/or (ii) more likely, the mollusc provides the essential plastid proteins. Under the latter scenario, genes supporting photosynthesis have been acquired by the animal via horizontal gene transfer and the encoded proteins are retargeted to the plastid. We sequenced the plastid genome and confirmed that it lacks the full complement of genes required for photosynthesis. In support of the second scenario, we demonstrated that a nuclear gene of oxygenic photosynthesis, psbO, is expressed in the sea slug and has integrated into the germline. The source of psbO in the sea slug is V. litorea because this sequence is identical from the predator and prey genomes. Evidence that the transferred gene has integrated into sea slug nuclear DNA comes from the finding of a highly diverged psbO 3 flanking sequence in the algal and mollusc nuclear homologues and gene absence from the mitochondrial genome of E. chlorotica. We demonstrate that foreign organelle retention generates metabolic novelty (''green animals'') and is explained by anastomosis of distinct branches of the tree of life driven by predation and horizontal gene transfer.
Under the endosymbiont hypothesis, over a billion years ago a heterotrophic eukaryote entered int... more Under the endosymbiont hypothesis, over a billion years ago a heterotrophic eukaryote entered into a symbiotic relationship with a cyanobacterium (the cyanobiont). This partnership culminated in the plastid that has spread to forms as diverse as plants and diatoms. However, why primary plastid acquisition has not been repeated multiple times remains unclear. Here, we report a possible answer to this question by showing that primary plastid endosymbiosis was likely to have been primed by the secretion in the host cytosol of effector proteins from intracellular Chlamydiales pathogens. We provide evidence suggesting that the cyanobiont might have rescued its afflicted host by feeding photosynthetic carbon into a chlamydiacontrolled assimilation pathway.
Abstract Phylogenomics, conventionally defined as the intersection of phylogenetics and genomics,... more Abstract Phylogenomics, conventionally defined as the intersection of phylogenetics and genomics, has become a key instrument in a wide spectrum of biological studies, including resolution of complex evolutionary relationships, assignment of taxonomic affiliation, prediction of protein molecular functions, and tracing horizontal gene transfer event.
Abstract My dissertation focuses on genome and functional evolution of photosynthetic eukaryotes ... more Abstract My dissertation focuses on genome and functional evolution of photosynthetic eukaryotes and the design and implementation of computational methods and tools to enable genome-wide studies to investigate these taxa. The work described here is grouped into two major topics, 1) endosymbiosis and genome evolution, and 2) harmful algal blooms. I discuss my work related to endosymbiosis and genome evolution in chapters 2-4. Chapters 5-6 cover the work related to harmful algal blooms.
Studies of photosynthetic eukaryotes have revealed that the evolution of plastids from cyanobacte... more Studies of photosynthetic eukaryotes have revealed that the evolution of plastids from cyanobacteria involved the recruitment of non-cyanobacterial proteins. Our phylogenetic survey of> 100 Arabidopsis nuclear-encoded plastid enzymes involved in amino acid biosynthesis identified only 21 unambiguous cyanobacterial-derived proteins. Some of the several non-cyanobacterial plastid enzymes have a shared phylogenetic origin in the three Plantae lineages.
Trench (1969) was the first to characterize the kleptoplastic (ie “stolen plastid”) relationship ... more Trench (1969) was the first to characterize the kleptoplastic (ie “stolen plastid”) relationship between the sacoglossan mollusc Elysia chlorotica and its algal prey (Vaucheria litorea). In contrast to E. chlorotica, which retains only the plastids of the alga in densely packed digestive tissue (Fig. 1), aquatic invertebrates (eg corals, clams, worms, tunicates) and the recently reported spotted salamander (Ambystoma maculatum; work of R.
The seafloor is a unique environment, which allows insights into how geochemical processes affect... more The seafloor is a unique environment, which allows insights into how geochemical processes affect the diversity of biological life. Among its diverse ecosystems are deep-sea brine pools-water bodies characterized by a unique combination of extreme conditions. The 'polyextremophiles' that constitute the microbial assemblage of these deep hot brines have not been comprehensively studied.
Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productiv... more Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial gene acquisition within chromalveolates. Therefore, analyses of gene content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall gene repertoire. As a single group of functionally related enzymes spanning two distinct gene families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of specific evolutionary associations among diatoms and other chromalveolates with various plastid-bearing and bacterial endosymbionts. Protein localization and activity, gene expression, and phylogenetic analyses indicate that the pennate diatom Phaeodactylum tricornutum contains five FBA genes with very little overall functional overlap. Three P. tricornutum FBAs, one class I and two class II, are plastid localized, and each appears to have a distinct evolutionary origin as well as function. Class I plastid FBA appears to have been acquired by chromalveolates from a red algal endosymbiont, whereas one copy of class II plastid FBA is likely to have originated from an ancient green algal endosymbiont. The other copy appears to be the result of a chromalveolate-specific gene duplication. Plastid FBA I and chromalveolate-specific class II plastid FBA are localized in the pyrenoid region of the chloroplast where they are associated with β-carbonic anhydrase, which is known to play a significant role in regulation of the diatom carbon concentrating mechanism. The two pyrenoid-associated FBAs are distinguished by contrasting gene expression profiles under nutrient limiting compared with optimal CO2 fixation conditions, suggestive of a distinct specialized function for each. Cytosolically localized FBAs in P. tricornutum likely play a role in glycolysis and cytoskeleton function and seem to have originated from the stramenopile host cell and from diatom-specific bacterial gene transfer, respectively.
Symbiotic animals containing green photobionts challenge the common perception that only plants a... more Symbiotic animals containing green photobionts challenge the common perception that only plants are capable of capturing the sun's rays and converting them into biological energy through photoautotrophic CO(2) fixation (photosynthesis). 'Solar-powered' sacoglossan molluscs, or sea slugs, have taken this type of symbiotic association one step further by solely harboring the photosynthetic organelle, the plastid (=chloroplast). One such sea slug, Elysia chlorotica, lives as a 'plant' when provided with only light and air as a result of acquiring plastids during feeding on its algal prey Vaucheria litorea. The captured plastids (kleptoplasts) are retained intracellularly in cells lining the digestive diverticula of the sea slug, a phenomenon sometimes referred to as kleptoplasty. Photosynthesis by the plastids provides E. chlorotica with energy and fixed carbon for its entire lifespan of ~10 months. The plastids are not transmitted vertically (i.e. are absent in eggs) and do not undergo division in the sea slug. However, de novo protein synthesis continues, including plastid- and nuclear-encoded plastid-targeted proteins, despite the apparent absence of algal nuclei. Here we discuss current data and provide hypotheses to explain how long-term photosynthetic activity is maintained by the kleptoplasts. This fascinating 'green animal' provides a unique model to study the evolution of photosynthesis in a multicellular heterotrophic organism.
Summary Symbiotic animals containing green photobionts challenge the common perception that only ... more Summary Symbiotic animals containing green photobionts challenge the common perception that only plants are capable of capturing the sun's rays and converting them into biological energy through photoautotrophic CO2 fixation (photosynthesis). ‘Solar-powered’ sacoglossan molluscs, or sea slugs, have taken this type of symbiotic association one step further by solely harboring the photosynthetic organelle, the plastid (=chloroplast). One such sea slug, Elysia chlorotica, lives as a ‘plant’ when provided with only light and air as a result of acquiring plastids during feeding on its algal prey Vaucheria litorea. The captured plastids (kleptoplasts) are retained intracellularly in cells lining the digestive diverticula of the sea slug, a phenomenon sometimes referred to as kleptoplasty. Photosynthesis by the plastids provides E. chlorotica with energy and fixed carbon for its entire lifespan of ∼10 months. The plastids are not transmitted vertically (i.e. are absent in eggs) and do ...
Experimental Materials Nor and Tnd standards of purity 101.08Ϯ0.85 (w/w) and 100.57Ϯ0.87 (w/w) re... more Experimental Materials Nor and Tnd standards of purity 101.08Ϯ0.85 (w/w) and 100.57Ϯ0.87 (w/w) respectively, according to European Pharmacopoeia 2005 methods, were kindly supplied by Pharaonia Pharmaceuticals (for Wockhardt, Egypt). Conaz ® tablets of batches 16929 and 16932 labeled to contain 400 mg Nor and 600 mg Tnd/tablet were from Pharaonia Pharmaceuticals (for Wockhardt, Egypt). Apparatus and Reagents A Shimadzu Ultraviolet/Visible spectrophotometer 1601-pc (Tokyo, Japan) with matched 1 cm quartz cells and connected to IBM compatible computer was used. Shimadzu-Dual wavelength lamp flying CS-9301 densitometer and ultraviolet short wavelength lamp (254 nm) were used. HPTLC plates were silica gel/TLC cards with fluorescent indicator (254 nm); layer thickness 0.2 mm; 20ϫ20 cm aluminum cards (Fluka). HPLC instrument was Hewlett Packard series 1100 equipped with a quaternary pump, diode array detector and a manual injector 20 ml loop (Minnesota, U.S.A.). Detection was carried at 280 nm and flow rate was 1 ml/min. Column used was m-Bondapack C18, 5 mm (300ϫ3.9 mm I.D.) was from Waters (Milford, U.S.A.). Ultrasonic was J.P. Selecta, s-a, CD. 300513, Spain. Methanol and acetonitrile (HPLC and Analytical grades) were from Lab scan Analytical Sciences (New Jersey, U.S.A.). Buffer used in mobile phase for LC method was 0.1 M sodium dihydrogen phosphate (Merck, Darmstadt, Germany) containing 0.005 M pentane sulfonic acid sodium salt and adjusted to pH 3.2 with phosphoric acid. Isopropanol and nbutanol were obtained from Lab scan analytical sciences (New Jersey, U.S.A.), pentane sulphonic acid was obtained from Acros organics (Geel, Belgium), phosphoric acid and concentrated ammonia were obtained from Riedel de-Haen (St. Louis, Missouri, U.S.A.). Preparation of Decarboxylated Nor Decarboxylated Nor was prepared according to the method reported by S. Z. El-Khateeb et al., 15) where the decarboxylated Nor was separated and collected from preparative TLC glass plates using the mobile phase applied in the TLC-densitometric method. The scratched degradant was dissolved in methanol and filtered. The filtrate was evaporated to dryness and the residue was collected. Stock Solutions Four stock solutions were prepared: Stock solution 1: 50 mg Nor was transferred into a 50-ml volumetric flask, dissolved in 2 ml
Under the endosymbiont hypothesis, over a billion years ago a heterotrophic eukaryote entered int... more Under the endosymbiont hypothesis, over a billion years ago a heterotrophic eukaryote entered into a symbiotic relationship with a cyanobacterium (the cyanobiont). This partnership culminated in the plastid that has spread to forms as diverse as plants and diatoms. However, why primary plastid acquisition has not been repeated multiple times remains unclear. Here, we report a possible answer to this question by showing that primary plastid endosymbiosis was likely to have been primed by the secretion in the host cytosol of effector proteins from intracellular Chlamydiales pathogens. We provide evidence suggesting that the cyanobiont might have rescued its afflicted host by feeding photosynthetic carbon into a chlamydia-controlled assimilation pathway.
There is great body of evidence showing a relationship between childhood adversity and psychosis ... more There is great body of evidence showing a relationship between childhood adversity and psychosis onset. Genetic factors moderate the association between childhood adversity and psychosis risk potentially by influencing biological and/or psychological reaction following exposure to adversity. In this review, we discuss studies identifying the specific genetic variants known to affect dopamine levels involved in this interaction. Our review shows that the catechol-O-methyltransferase (COMT), dopamine D2 receptor (DRD2), AKT1 gene play a key role in mediating the relationship between childhood adversity and development of psychosis. We have also found conflicting findings on the impact of dopamine genes on the relationship between childhood adversity and development of psychosis, suggesting that other genetic and environmental factors should be taken into account. We here discuss the implications of our findings and future directions.
Red seaweeds are key components of coastal ecosystems and are economically important as food and ... more Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.
My dissertation focuses on genome and functional evolution of photosynthetic eukaryotes and the d... more My dissertation focuses on genome and functional evolution of photosynthetic eukaryotes and the design and implementation of computational methods and tools to enable genome-wide studies to investigate these taxa.
Phylogenomics, conventionally defined as the intersection of phylogenetics and genomics, has beco... more Phylogenomics, conventionally defined as the intersection of phylogenetics and genomics, has become a key instrument in a wide spectrum of biological studies, including resolution of complex evolutionary relationships, assignment of taxonomic affiliation, prediction of protein molecular functions, and tracing horizontal gene transfer event. Here, we introduce an open-source phylogenomic pipeline, iTree, which automates the execution of phylogenetic analyses under multithreaded and grid-computing environments, providing a scalable high-throughput platform for performing genome-wide evolutionary analyses. Furthermore, we describe the results of two applications of using iTree: (1) taxonomic assignment of 16S ribosomal RNA sequences from human oral metagenomic samples and (2) detection of horizontal gene transfer in microbial genomes.
The seafloor is a unique environment, which allows insights into how geochemical processes affect... more The seafloor is a unique environment, which allows insights into how geochemical processes affect the diversity of biological life. Among its diverse ecosystems are deep-sea brine pools -water bodies characterized by a unique combination of extreme conditions. The 'polyextremophiles' that constitute the microbial assemblage of these deep hot brines have not been comprehensively studied. We report a comparative taxonomic analysis of the prokaryotic communities of the sediments directly below the Red Sea brine pools, namely, Atlantis II, Discovery, Chain Deep, and an adjacent brine-influenced site. Analyses of sediment samples and high-throughput pyrosequencing of PCR-amplified environmental 16S ribosomal RNA genes (16S rDNA) revealed that one sulfur (S)-rich Atlantis II and one nitrogen (N)-rich Discovery Deep section contained distinct microbial populations that differed from those found in the other sediment samples examined. Proteobacteria, Actinobacteria, Cyanobacteria, Deferribacteres, and Euryarchaeota were the most abundant bacterial and archaeal phyla in both the S-and N-rich sections. Relative abundance-based hierarchical clustering of the 16S rDNA pyrotags assigned to major taxonomic groups allowed us to categorize the archaeal and bacterial communities into three major and distinct groups; group I was unique to the S-rich Atlantis II section (ATII-1), group II was characteristic for the N-rich Discovery sample (DD-1), and group III reflected the composition of the remaining sediments. Many of the groups detected in the S-rich Atlantis II section are likely to play a dominant role in the cycling of methane and sulfur due to their phylogenetic affiliations with bacteria and archaea involved in anaerobic methane oxidation and sulfate reduction.
Proceedings of The National Academy of Sciences, 2008
The sea slug Elysia chlorotica acquires plastids by ingestion of its algal food source Vaucheria ... more The sea slug Elysia chlorotica acquires plastids by ingestion of its algal food source Vaucheria litorea. Organelles are sequestered in the mollusc's digestive epithelium, where they photosynthesize for months in the absence of algal nucleocytoplasm. This is perplexing because plastid metabolism depends on the nuclear genome for >90% of the needed proteins. Two possible explanations for the persistence of photosynthesis in the sea slug are (i) the ability of V. litorea plastids to retain genetic autonomy and/or (ii) more likely, the mollusc provides the essential plastid proteins. Under the latter scenario, genes supporting photosynthesis have been acquired by the animal via horizontal gene transfer and the encoded proteins are retargeted to the plastid. We sequenced the plastid genome and confirmed that it lacks the full complement of genes required for photosynthesis. In support of the second scenario, we demonstrated that a nuclear gene of oxygenic photosynthesis, psbO, is expressed in the sea slug and has integrated into the germline. The source of psbO in the sea slug is V. litorea because this sequence is identical from the predator and prey genomes. Evidence that the transferred gene has integrated into sea slug nuclear DNA comes from the finding of a highly diverged psbO 3 flanking sequence in the algal and mollusc nuclear homologues and gene absence from the mitochondrial genome of E. chlorotica. We demonstrate that foreign organelle retention generates metabolic novelty (''green animals'') and is explained by anastomosis of distinct branches of the tree of life driven by predation and horizontal gene transfer.
Under the endosymbiont hypothesis, over a billion years ago a heterotrophic eukaryote entered int... more Under the endosymbiont hypothesis, over a billion years ago a heterotrophic eukaryote entered into a symbiotic relationship with a cyanobacterium (the cyanobiont). This partnership culminated in the plastid that has spread to forms as diverse as plants and diatoms. However, why primary plastid acquisition has not been repeated multiple times remains unclear. Here, we report a possible answer to this question by showing that primary plastid endosymbiosis was likely to have been primed by the secretion in the host cytosol of effector proteins from intracellular Chlamydiales pathogens. We provide evidence suggesting that the cyanobiont might have rescued its afflicted host by feeding photosynthetic carbon into a chlamydiacontrolled assimilation pathway.
Abstract Phylogenomics, conventionally defined as the intersection of phylogenetics and genomics,... more Abstract Phylogenomics, conventionally defined as the intersection of phylogenetics and genomics, has become a key instrument in a wide spectrum of biological studies, including resolution of complex evolutionary relationships, assignment of taxonomic affiliation, prediction of protein molecular functions, and tracing horizontal gene transfer event.
Abstract My dissertation focuses on genome and functional evolution of photosynthetic eukaryotes ... more Abstract My dissertation focuses on genome and functional evolution of photosynthetic eukaryotes and the design and implementation of computational methods and tools to enable genome-wide studies to investigate these taxa. The work described here is grouped into two major topics, 1) endosymbiosis and genome evolution, and 2) harmful algal blooms. I discuss my work related to endosymbiosis and genome evolution in chapters 2-4. Chapters 5-6 cover the work related to harmful algal blooms.
Studies of photosynthetic eukaryotes have revealed that the evolution of plastids from cyanobacte... more Studies of photosynthetic eukaryotes have revealed that the evolution of plastids from cyanobacteria involved the recruitment of non-cyanobacterial proteins. Our phylogenetic survey of> 100 Arabidopsis nuclear-encoded plastid enzymes involved in amino acid biosynthesis identified only 21 unambiguous cyanobacterial-derived proteins. Some of the several non-cyanobacterial plastid enzymes have a shared phylogenetic origin in the three Plantae lineages.
Trench (1969) was the first to characterize the kleptoplastic (ie “stolen plastid”) relationship ... more Trench (1969) was the first to characterize the kleptoplastic (ie “stolen plastid”) relationship between the sacoglossan mollusc Elysia chlorotica and its algal prey (Vaucheria litorea). In contrast to E. chlorotica, which retains only the plastids of the alga in densely packed digestive tissue (Fig. 1), aquatic invertebrates (eg corals, clams, worms, tunicates) and the recently reported spotted salamander (Ambystoma maculatum; work of R.
The seafloor is a unique environment, which allows insights into how geochemical processes affect... more The seafloor is a unique environment, which allows insights into how geochemical processes affect the diversity of biological life. Among its diverse ecosystems are deep-sea brine pools-water bodies characterized by a unique combination of extreme conditions. The 'polyextremophiles' that constitute the microbial assemblage of these deep hot brines have not been comprehensively studied.
Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productiv... more Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial gene acquisition within chromalveolates. Therefore, analyses of gene content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall gene repertoire. As a single group of functionally related enzymes spanning two distinct gene families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of specific evolutionary associations among diatoms and other chromalveolates with various plastid-bearing and bacterial endosymbionts. Protein localization and activity, gene expression, and phylogenetic analyses indicate that the pennate diatom Phaeodactylum tricornutum contains five FBA genes with very little overall functional overlap. Three P. tricornutum FBAs, one class I and two class II, are plastid localized, and each appears to have a distinct evolutionary origin as well as function. Class I plastid FBA appears to have been acquired by chromalveolates from a red algal endosymbiont, whereas one copy of class II plastid FBA is likely to have originated from an ancient green algal endosymbiont. The other copy appears to be the result of a chromalveolate-specific gene duplication. Plastid FBA I and chromalveolate-specific class II plastid FBA are localized in the pyrenoid region of the chloroplast where they are associated with β-carbonic anhydrase, which is known to play a significant role in regulation of the diatom carbon concentrating mechanism. The two pyrenoid-associated FBAs are distinguished by contrasting gene expression profiles under nutrient limiting compared with optimal CO2 fixation conditions, suggestive of a distinct specialized function for each. Cytosolically localized FBAs in P. tricornutum likely play a role in glycolysis and cytoskeleton function and seem to have originated from the stramenopile host cell and from diatom-specific bacterial gene transfer, respectively.
Symbiotic animals containing green photobionts challenge the common perception that only plants a... more Symbiotic animals containing green photobionts challenge the common perception that only plants are capable of capturing the sun's rays and converting them into biological energy through photoautotrophic CO(2) fixation (photosynthesis). 'Solar-powered' sacoglossan molluscs, or sea slugs, have taken this type of symbiotic association one step further by solely harboring the photosynthetic organelle, the plastid (=chloroplast). One such sea slug, Elysia chlorotica, lives as a 'plant' when provided with only light and air as a result of acquiring plastids during feeding on its algal prey Vaucheria litorea. The captured plastids (kleptoplasts) are retained intracellularly in cells lining the digestive diverticula of the sea slug, a phenomenon sometimes referred to as kleptoplasty. Photosynthesis by the plastids provides E. chlorotica with energy and fixed carbon for its entire lifespan of ~10 months. The plastids are not transmitted vertically (i.e. are absent in eggs) and do not undergo division in the sea slug. However, de novo protein synthesis continues, including plastid- and nuclear-encoded plastid-targeted proteins, despite the apparent absence of algal nuclei. Here we discuss current data and provide hypotheses to explain how long-term photosynthetic activity is maintained by the kleptoplasts. This fascinating 'green animal' provides a unique model to study the evolution of photosynthesis in a multicellular heterotrophic organism.
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Papers by Ahmed Moustafa