抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

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Phytozome: a comparative platform for green plant genomics

Microalgae represent an exceptionally diverse but highly specialized group of micro-organisms adapted to various ecological habitats. Many microalgae have the ability to produce substantial amounts (e.g. 20-50% dry cell weight) of triacylglycerols (TAG) as a storage lipid under photo-oxidative stress or other adverse environmental conditions. Fatty acids, the building blocks for TAGs and all other cellular lipids, are synthesized in the chloroplast using a single set of enzymes, of which acetyl CoA carboxylase (ACCase) is key in regulating fatty acid synthesis rates. However, the expression of genes involved in fatty acid synthesis is poorly understood in microalgae. Synthesis and sequestration of TAG into cytosolic lipid bodies appear to be a protective mechanism by which algal cells cope with stress conditions, but little is known about regulation of TAG formation at the molecular and cellular level. While the concept of using microalgae as an alternative and renewable source of lipid-rich biomass feedstock for biofuels has been explored over the past few decades, a scalable, commercially viable system has yet to emerge. Today, the production of algal oil is primarily confined to high-value specialty oils with nutritional value, rather than commodity oils for biofuel. This review provides a brief summary of the current knowledge on oleaginous algae and their fatty acid and TAG biosynthesis, algal model systems and genomic approaches to a better understanding of TAG production, and a historical perspective and path forward for microalgae-based biofuel research and commercialization.

https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1365-313X.2008.03492.x

Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances

The use of fossil fuels is now widely accepted as unsustainable due to depleting resources and the accumulation of greenhouse gases in the environment that have already exceeded the “dangerously high” threshold of 450 ppm CO2-e. To achieve environmental and economic sustainability, fuel production processes are required that are not only renewable, but also capable of sequestering atmospheric CO2. Currently, nearly all renewable energy sources (e.g. hydroelectric, solar, wind, tidal, geothermal) target the electricity market, while fuels make up a much larger share of the global energy demand (∼66%). Biofuels are therefore rapidly being developed. Second generation microalgal systems have the advantage that they can produce a wide range of feedstocks for the production of biodiesel, bioethanol, biomethane and biohydrogen. Biodiesel is currently produced from oil synthesized by conventional fuel crops that harvest the sun’s energy and store it as chemical energy. This presents a route for renewable and carbon-neutral fuel production. However, current supplies from oil crops and animal fats account for only approximately 0.3% of the current demand for transport fuels. Increasing biofuel production on arable land could have severe consequences for global food supply. In contrast, producing biodiesel from algae is widely regarded as one of the most efficient ways of generating biofuels and also appears to represent the only current renewable source of oil that could meet the global demand for transport fuels. The main advantages of second generation microalgal systems are that they: (1) Have a higher photon conversion efficiency (as evidenced by increased biomass yields per hectare): (2) Can be harvested batch-wise nearly all-year-round, providing a reliable and continuous supply of oil: (3) Can utilize salt and waste water streams, thereby greatly reducing freshwater use: (4) Can couple CO2-neutral fuel production with CO2 sequestration: (5) Produce non-toxic and highly biodegradable biofuels. Current limitations exist mainly in the harvesting process and in the supply of CO2 for high efficiency production. This review provides a brief overview of second generation biodiesel production systems using microalgae.

https://www.springer.com/cda/content/document/cda_downloaddocument/BioEnergyResearch_Second+Generation+Biofuels+High-Efficiency+Microalgae+for+Biodiesel+Production.pdf?SGWID=0-0-45-1347846-0

Second generation biofuels: high-efficiency microalgae for biodiesel production

1. Light and Energy. 2. Organization and Structure of Photosynthetic Systems. 3. History and Development of Photosynthesis. 4. Photosynthetic Pigments-Structure and Spectroscopy. 5. Antenna Complexes and Energy Transfer Processes. 6. Reaction Center Complexes. 7. Electron Transfer Pathways and Components. 8. Chemiosmotic Coupling and ATP Synthesis. 9. Carbon Metabolism. 10. Genetics, Assembly and Regulation of Photosynthetic. Systems. 11. Origin and Evolution of Photosynthesis. Appendix 1. Light, Energy and Kinetics

Molecular mechanisms of photosynthesis

Random insertional mutagenesis of Chlamydomonas reinhardtii using drug resistance cassettes has contributed to the generation of tens of thousands of transformants in dozens of labs around the world. In many instances these insertional mutants have helped elucidate the genetic basis of various physiological processes in this model organism. Unfortunately, the insertion sites of many interesting mutants are never defined due to experimental difficulties in establishing the location of the inserted cassette in the Chlamydomonas genome. It is fairly common that several months, or even years of work are conducted with no result. Here we describe a robust method to identify the location of the inserted DNA cassette in the Chlamydomonas genome. Insertional mutants were generated using a DNA cassette that confers paromomycin resistance. This protocol identified the cassette insertion site for greater than 80% of the transformants. In the majority of cases the insertion event was found to be simple, without large deletions of flanking genomic DNA. Multiple insertions were observed in less than 10% of recovered transformants. The method is quick, relatively inexpensive and does not require any special equipment beyond an electroporator. The protocol was tailored to ensure that the sequence of the Chlamydomonas genomic DNA flanking the random insertion is consistently obtained in a high proportion of transformants. A detailed protocol is presented to aid in the experimental design and implementation of mutant screens in Chlamydomonas.

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A robust protocol for efficient generation, and genomic characterization of insertional mutants of Chlamydomonas reinhardtii

The regulation of the photorespiratory pathway in Chlamydomonas reinhardtii Dangeard during a shift from high- to low-CO2 conditions was investigated. To this end, a set of C. reinhardtii cDNA sequences for known photorespiratory enzymes was assembled using the Chlamydomonas expressed sequence tag database and primary sequencing data. Expression data indicates that there is a rapid and coordinated induction of photorespiratory and CCM gene expression during a time course switch from high-CO2 conditions (5% (v/v)) to low-CO2 conditions (0.038% (v/v)). While the expression of photorespiratory and CCM genes are coordinated during the initial change in CO2 level, the response of these two sets of genes to the CO2 level is not identical. Unlike the sustained high levels of CCM mRNAs seen under low CO2 conditions, photorespiratory mRNAs show a transient increase in abundance in time course experiments. In addition, the expression of these photorespiratory genes is reduced in cia5, a C. reinhardtii strain that l...

/pdf/regulation-of-the-expression-of-photorespiratory-genes-in-m0rlexm428.pdf

Regulation of the expression of photorespiratory genes in Chlamydomonas reinhardtii

Spinach chloroplast thylakoids treated in the light with bifunctional maleimides were previously shown to be uncoupled. The increase in proton permeability by these reagents is caused by the cross-linking of an accessible group on the γ subunit of coupling factor 1 (CF1) to a group that becomes exposed to reaction with maleimides only when the thylakoids are energized. In this study, several bifunctional maleimides, includingo-,m-, andp-phenylenebismaleimides, 2,3- and 1,5-naphthalenebismaleimides, and azophenylbismaleimide, were tested for their ability to form cross-links and to uncouple photophosphorylation. These reagents form cross-links from about 6 to 19 A. Each reagent was found to form cross-links in the light and to inhibit photophosphorylation. However, the effectiveness of these compounds as uncouplers decreased as the distance between the cross-linked groups increased, indicating that the distance between two groups on the γ subunit of CF1 can regulate proton flux through the membrane. Monofunctional maleimides cause a light-dependent energy transfer type of inhibition of photophosphorylation. Although this inhibition was correlated to the reaction of the maleimide with a group on the γ subunit that is exposed only in energized thylakoids, the accessible group on this subunit was also modified by the reagent. However, we show here that the accessible group plays no role in the inhibition of photophosphorylation. This group may be blocked by incubating thylakoids in the dark with methyl methanethiolsulfonate. The light-dependent inhibition of photophosphorylation byN-ethylmaleimide was unaffected by this treatment or by the subsequent removal of the methanethiol moiety from the accessible group.

The distance between thiol groups in the γ subunit of coupling factor 1 influences the proton permeability of thylakoid membranes

Unicellular algae acquire the ability to raise their internal CO2 concentrations under low-CO2 conditions because of the presence of a CO2 concentrating mechanism (CCM). In Chlamydomonas reinhardtii, this mechanism is induced when cells grown in high-CO2 conditions are switched to low-CO2 conditions. To elucidate the genes and proteins involved in this mechanism, we constructed a cDNA library from low CO2 adapted cells and differentially screened the library for cDNAs upregulated under low-CO2 conditions. Earlier studies identified six classes of clones specific to low CO2 adapting cells. To identify other genes and proteins playing a role in this mechanism, we have systematically characterized the cDNA clones that appear to be upregulated by low-CO2 adaptation but do not cross-hybridize with the six previously identified classes. We identified seven new classes of clones that are distinctly upregulated in low-CO2 conditions. These clones were checked by Northern analyses, sequencing, and homology studies...

Chlamydomonas reinhardtii cDNAs upregulated in low-CO2 conditions: expression and analyses

Ergosterol and 7-dehydroporiferasterol are the predominant sterols in the membranes of the alga Chlamydomonas reinhardtii Dangeard. Ergosterol is primarily found in most fungi, which produce their end-product sterols by way of the intermediate lanosterol. In contrast, plants rarely make ergosterol and plant sterols are made via the intermediate cycloartenol. The cycloartenol-lanosterol bifurcation has been used as a means to evolutionarily categorize species based on their sterol production. Use of bioinformatics has revealed that the green alga, C. reinhardtii is probably producing sterols using a pathway very similar to that of higher plants. The Chlamydomonas genome was searched for genes that encoded proteins exhibiting high similarity to sterol biosynthetic proteins in the higher plant Arabidopsis thaliana or the yeast Saccharomyces cerevisiae. Genes with the greatest similarity were chosen and annotated. To establish whether these genes were expressed, the presence of their transcripts was d...

/pdf/a-model-for-the-ergosterol-biosynthetic-pathway-in-47503pcmma.pdf

James V. Moroney

Papers

A robust protocol for efficient generation, and genomic characterization of insertional mutants of Chlamydomonas reinhardtii

Regulation of the expression of photorespiratory genes in Chlamydomonas reinhardtii

The distance between thiol groups in the γ subunit of coupling factor 1 influences the proton permeability of thylakoid membranes

Chlamydomonas reinhardtii cDNAs upregulated in low-CO2 conditions: expression and analyses

A model for the ergosterol biosynthetic pathway in Chlamydomonas reinhardtii