Phylogeny and Molecular Evolution of the Green Algae

The green lineage (Viridiplantae) comprises the green algae and their descendants the land plants, and is one of the major groups of oxygenic photosynthetic eukaryotes. Current hypotheses posit the early divergence of two discrete clades from an ancestral green flagellate. One clade, the Chlorophyta, comprises the early diverging prasinophytes, which gave rise to the core chlorophytes. The other clade, the Streptophyta, includes the charophyte green algae from which the land plants evolved. Multi-marker and genome scale phylogenetic studies have greatly improved our understanding of broad-scale relationships of the green lineage, yet many questions persist, including the branching orders of the prasinophyte lineages, the relationships among core chlorophyte clades (Chlorodendrophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae), and the relationships among the streptophytes. Current phylogenetic hypotheses provide an evolutionary framework for molecular evolutionary studies and comparative genomics. This review summarizes our current understanding of organelle genome evolution in the green algae, genomic insights into the ecology of oceanic picoplanktonic prasinophytes, molecular mechanisms underlying the evolution of complexity in volvocine green algae, and the evolution of genetic codes and the translational apparatus in green seaweeds. Finally, we discuss molecular evolution in the streptophyte lineage, emphasizing the genetic facilitation of land plant origins.     

Molecular Phylogenies and Evolution of crt Genes in Algae

ABSTRACT

The carotenoids constitute the most widespread class of pigments in nature. Most previous work has concentrated on the identification and characterization of their chemical physical properties and bioavailability. In recent years, significant amounts of research have been conducted in an attempt to analyze the genes and the molecular regulation of the genes involved in the biosynthesis of carotenoids. However, it is important not to lose sight of the early evolution of carotenoid biosynthesis. One of the major obstacles in understanding the evolution of the respective enzymes and their patterns of selection is a lack of a well-supported phylogenic analysis. In the present research, a major long-term objective was to provide a clearer picture of the evolutionary history of genes, together with an evaluation of the patterns of selection in algae. These phylogenies will be important in studies characterizing the evolution of algae. The gene sequences of the enzymes involved in the major steps of the carotenoid biosynthetic pathway in algae (cyanobacteria, rhofophyta, chlorophyta) have been analyzed. Phylogenetic relationships among protein-coding DNA sequences were reconstructed by neighbor-joining (NJ) analysis for the respective carotenoid biosynthetic pathway genes (crt) in algae. The analysis also contains an estimation of the rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d_N), synonymous nucleotide substitution per synonymous site (d_S), and the ratio of nonsynonmous (d_N/d_S) for the test of selection patterns. The phylogenetic trees show that the taxa of some genera have a closer evolutionary relationship with other genera in some gene sequences, which suggests a common ancient origin and that lateral gene transfer has occurred among unrelated genera. The d_N values of crt genes in the early pathway are relatively low, while those of the following steps are slightly higher, while the d_N values of crt genes in chlorophyta are higher than those in cyanobacteria. Most of the d_N/d_S values exceed 1. The phylogenetic analysis revealed that lateral gene transfer may have taken place across algal genomes and the d_N values suggest that most of the early crt genes are well conserved compared to the later crt genes. Furthermore, d_N values also revealed that the crt genes of chlorophyta are more evolutionary than cyanobacteria. The amino acids' changes are mostly adaptive evolution under the influence of positive diversity selection.     

Functional Divergence and Convergent Evolution in the Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenases of Diverse Eukaryotic Algae

Background

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key enzyme of the glycolytic pathway, reversibly catalyzing the sixth step of glycolysis and concurrently reducing the coenzyme NAD⁺ to NADH. In photosynthetic organisms a GAPDH paralog (Gap2 in Cyanobacteria, GapA in most photosynthetic eukaryotes) functions in the Calvin cycle, performing the reverse of the glycolytic reaction and using the coenzyme NADPH preferentially. In a number of photosynthetic eukaryotes that acquired their plastid by the secondary endosymbiosis of a eukaryotic red alga (Alveolates, haptophytes, cryptomonads and stramenopiles) GapA has been apparently replaced with a paralog of the host’s own cytosolic GAPDH (GapC1). Plastid GapC1 and GapA therefore represent two independent cases of functional divergence and adaptations to the Calvin cycle entailing a shift in subcellular targeting and a shift in binding preference from NAD⁺ to NADPH.

Methods

We used the programs FunDi, GroupSim, and Difference Evolutionary-Trace to detect sites involved in the functional divergence of these two groups of GAPDH sequences and to identify potential cases of convergent evolution in the Calvin-cycle adapted GapA and GapC1 families. Sites identified as being functionally divergent by all or some of these programs were then investigated with respect to their possible roles in the structure and function of both glycolytic and plastid-targeted GAPDH isoforms.

Conclusions

In this work we found substantial evidence for convergent evolution in GapA/B and GapC1. In many cases sites in GAPDHs of these groups converged on identical amino acid residues in specific positions of the protein known to play a role in the function and regulation of plastid-functioning enzymes relative to their cytosolic counterparts. In addition, we demonstrate that bioinformatic software like FunDi are important tools for the generation of meaningful biological hypotheses that can then be tested with direct experimental techniques.     

Biosynthesis of Carotenoids in the Chloroplasts of Algae and Higher Plants

Physiological, biochemical, and genetic aspects of carotenoid biosynthesis in the chloroplast membranes of green algae and higher plants are discussed starting from the earliest stages of biosynthesis of key C₅-isoprene units. The latter are synthesized either from acetate (C₂) to mevalonic acid (C₆) or from glucose (C₆) by forming glyceraldehyde 3-phosphate (C₃) and pyruvate decarboxylation product (C₂) through intermediate compounds to isopentenyl diphosphate (C₅). In all organisms, the further carotenoid synthesis from isopentenyl diphosphate and its isomer dimethylallyl diphosphate (C₅) proceeds through their transformation into geranyl diphosphate (C₁₀), farnesyl diphosphate (C₁₅), geranylgeranyl diphosphate (C₂₀) and phytoene (C₄₀). Phytoene desaturation (dehydrogenation) to carotene, neurosporene, and lycopene, and all steps of their cyclization to , and carotenes are discussed in detail. The synthesis of xanthophylls in chloroplasts is presented as the sequential formation of hydroxy-, epoxy- and oxo- groups. Genetic control of biosynthesis, as well as the localization and functional role of carotenoids in the chloroplast membranes of plants and algae are briefly discussed.     

Scavenging of Hydrogen Peroxide in Prokaryotic and Eukaryotic Algae: Acquisition of Ascorbate Peroxidase during the Evolution of Cyanobacteria

Ascorbate (AsA) peroxidase was found in six species of cyanobacteriaamong ten species tested. Upon the addition of H₂¹⁸O₂ to thecells of AsA peroxidase-containing cyanobacteria, ¹⁶O₂ derivedfrom water and ¹⁸O₂ derived from H₂^I8O₂ were evolved in thelight. The evolution of ¹⁶O₂ was inhibited by DCMU and did notoccur in the dark, but ^I8O₂ was evolved even in the dark orin the presence of DCMU. Similar light-dependent evolution of¹⁶O₂ was observed in the cells of AsA peroxidase-containingEuglena and Chlamydomonas. However, the cells of AsA perox-idase-lackingcyanobacteria evolved only ¹⁸O₂ in either the light or dark.Furthermore, the quenching of chlorophyll fluorescence inducedby hydrogen peroxide was observed only in the cells of the AsAperoxidase-containing Synechocystis 6803, and not in the cellsof Anacystis nidulans which lacks AsA peroxidase. Thus, cyanobacteriacan be divided into two groups, those that has and those thatlacks AsA peroxidase. The first group scavenges hydrogen peroxidewith the peroxidase using a photoreductant as the electron donor,and the second group only scavenges hydrogen peroxide with catalase. (Received July 23, 1990; Accepted October 18, 1990)     

Genome-Wide Analysis of Biotin Biosynthesis in Eukaryotic Photosynthetic Algae

Biotin is a cofactor responsible for carbon dioxide transfer in several carboxylase enzymes, which play a significant role in various metabolic reactions such as fatty acid synthesis, branched chain amino acid catabolism, and gluconeogenesis. Biotin is also involved in citric acid cycle, which is the process of biochemical energy generation during aerobic respiration. Though the function of biotin in the growth of algae has been extensively investigated, little is known about the biosynthetic routes of biotin in the algal kingdom. In the present study, 44 biotin biosynthesis-related genes were identified from 14 eukaryotic photosynthetic algal genomes by BLASTP and TBLASN programs. A comprehensive analysis was performed to characterize distribution, phylogeny, structure domains, and coevolution patterns of those genes. Forty-four biotin biosynthesis-related enzymes (BBREs) were found to be distributed in three groups: 7-keto-8-aminopelargonic acid synthase, diaminopelargonic acid synthase/dethiobiotin synthetase, and biotin synthase. Structure domains were considerably conserved among the subfamilies of BBREs. The intramolecular coevolutionary sites are widely distributed in biotin synthase. The present study provides new insights into the origin and evolution of biotin biosynthetic pathways in eukaryotic photosynthetic algae. Furthermore, the characterization of biotin biosynthesis-related genes from algae will promote the identification and functional studies of BBREs.     

Lineage-Specific Domain Fusion in the Evolution of Purine Nucleotide Cyclases in Cyanobacteria

Cyclic nucleotides (both cAMP and cGMP) play extremely important roles in cyanobacteria, such as regulating heterocyst formation, respiration, or gliding. Catalyzing the formation of cAMP and cGMP from ATP and GTP is a group of functionally important enzymes named adenylate cyclases and guanylate cyclases, respectively. To understand their evolutionary patterns, in this study, we presented a systematic analysis of all the cyclases in cyanobacterial genomes. We found that different cyanobacteria had various numbers of cyclases in view of their remarkable diversities in genome size and physiology. Most of these cyclases exhibited distinct domain architectures, which implies the versatile functions of cyanobacterial cyclases. Mapping the whole set of cyclase domain architectures from diverse prokaryotic organisms to their phylogenetic tree and detailed phylogenetic analysis of cyclase catalytic domains revealed that lineage-specific domain recruitment appeared to be the most prevailing pattern contributing to the great variability of cyanobacterial cyclase domain architectures. However, other scenarios, such as gene duplication, also occurred during the evolution of cyanobacterial cyclases. Sequence divergence seemed to contribute to the origin of putative guanylate cyclases which were found only in cyanobacteria. In conclusion, the comprehensive survey of cyclases in cyanobacteria provides novel insight into their potential evolutionary mechanisms and further functional implications.     

Molecular Markers of Cell Position in Avian Retina are Involved in Synapse Formation

Molecules that identify cell type and position in the nervoussystem were detected by monoclonal antibodies. One molecule,TOP, is distributed in a 35-fold topographic gradient from thedorsoposterior margin to the ventro-anterior margin of avianretina. The gradient is present in young embryos, increaseswith retinal growth, and persists in the adult. TOP moleculesare present on most or all cells of retina. The number of TOPmolecules detected per cell varies continuously along the axisof the antigen gradient. Thus, TOP can be used to identify positionin the plane of retina along that axis. Other antigens thatidentify cell type and position across the thickness of retinaalso were detected. Molecules that mark such cellular organizationmay represent a neuronal recognition system. Antibodies were used to examine the role of markers of cellposition in development of the nervous system. Antibody to TOPfrom hybridoma cells that were injected into in vivo embryoeyes diffused into the retina and bound in a topographic gradientof [Ab- TOP] complexes. Synapse formation in retina was inhibitedin the presence of anti-TOP antibody. This suggests that TOPis involved in synapse formation and that recognition of positionby neurons is necessary for normal synapse formation.     

Molecular Evolution of the Two-Component System BvgAS Involved in Virulence Regulation in Bordetella

The whooping cough agent Bordetella pertussis is closely related to Bordetella bronchiseptica, which is responsible for chronic respiratory infections in various mammals and is occasionally found in humans, and to Bordetella parapertussis, one lineage of which causes mild whooping cough in humans and the other ovine respiratory infections. All three species produce similar sets of virulence factors that are co-regulated by the two-component system BvgAS. We characterized the molecular diversity of BvgAS in Bordetella by sequencing the two genes from a large number of diverse isolates. The response regulator BvgA is virtually invariant, indicating strong functional constraints. In contrast, the multi-domain sensor kinase BvgS has evolved into two different types. The pertussis type is found in B. pertussis and in a lineage of essentially human-associated B. bronchiseptica, while the bronchiseptica type is associated with the majority of B. bronchiseptica and both ovine and human B. parapertussis. BvgS is monomorphic in B. pertussis, suggesting optimal adaptation or a recent population bottleneck. The degree of diversity of the bronchiseptica type BvgS is markedly different between domains, indicating distinct evolutionary pressures. Thus, absolute conservation of the putative solute-binding cavities of the two periplasmic Venus Fly Trap (VFT) domains suggests that common signals are perceived in all three species, while the external surfaces of these domains vary more extensively. Co-evolution of the surfaces of the two VFT domains in each type and domain swapping experiments indicate that signal transduction in the periplasmic region may be type-specific. The two distinct evolutionary solutions for BvgS confirm that B. pertussis has emerged from a specific B. bronchiseptica lineage. The invariant regions of BvgS point to essential parts for its molecular mechanism, while the variable regions may indicate adaptations to different lifestyles. The repertoire of BvgS sequences will pave the way for functional analyses of this prototypic system.     

Eukaryotic Algae Associated with Mid-Proterozoic Black Chert in Northern China

During the past two decades, Precambrian research, especially in the respect of the occurfence of microbial fossils in silicified rocks has been achieved. It is still in argument, however, at what time the origin of the eukaryote, one of the major events in biological evolution appeared according to the different criteria of the low, er eukaryotic organism fossils identified. The difference between prokaryotic and eukaryotic algal fossils in the cell size of structure and morphological colony and the model of their reproduction in biologic evolution is interpreted based on the knowledge about living lower organisms in this paper. Eight genera and eight species of eukaryotic algal fossils, including three genera and three species (Proto- cosmarium panduratum, Closteriopsis taihangensis and Phyllophycoma sinensis) newly descover ed in black stromatolitic chert from Gaoyuzhuang Formation, Lingqiu, Shanxi Province, China, which is about 1,400–1,600 My in age are described and named. All of these are characterized by the big cell size and complex structure of colony in which the cells have been divided into different function in physiology, and some of them produce endospore and autospore which are comparable with their mother cell or colony in morphology. According to the morphological characters of complex and diverse microfossils, it is assumed that the evolution of eukaryotic organisms had been achieved and even evolved up to a higher level at least before 1,600 million years.     

番茄红素环化酶基因shRNA真核表达质粒的构建及鉴定

目的利用RNA干扰技术,构建靶向番茄红素环化酶基因(CarR)的干扰质粒,为选择性抑制番茄红素环化酶活性以提高番茄红素产量,奠定基础。方法用DNA重组技术将针对三孢布拉氏霉菌CarR的不同部位所设计的3对shRNA序列克隆到真核表达质粒mU6 pro中,构建CarR shRNA表达质粒重组体mU6 CarR shRNA1、2、3,转化DH5а菌株扩增。提取质粒行酶切鉴定后,进行测序分析。结果3个CarR shRNA表达载体mU6 CarR shRNA1、2、3经限制性酶切及部分序列分析证明基因插入正确。结论成功构建了CarR shRNA表达载体mU6 CarR shRNA,重组体的成功构建为研究CarR靶向RNA干扰番茄红素的环化打下基础。     

Molecular View of 43 S Complex Formation and Start Site Selection in Eukaryotic Translation Initiation

A central step to high fidelity protein synthesis is selection of the proper start codon. Recent structural, biochemical, and genetic analyses have provided molecular insights into the coordinated activities of the initiation factors in start codon selection. A molecular model is emerging in which start codon recognition is linked to dynamic reorganization of factors on the ribosome and structural changes in the ribosome itself.     

嗅觉的分子生物学基础

嗅觉是动物对挥发性物质的感觉过程。嗅质分子、嗅质结合蛋白以及嗅质受体是完成嗅觉感受最初阶段的3个要素。嗅质分子一般为小分子挥发性物质,需要先与嗅质结合蛋白结合以助溶,再与受体结合,通过与视觉类似的过程在嗅觉神经元中引起电信号：该电信号传至中枢神经系统,产生嗅觉。嗅质受体编码基因数目庞大,其假基因化程度与物种生存对嗅觉的依赖程度存在一定关系。     

Evolution of Copper Transporting ATPases in Eukaryotic Organisms

Copper is an essential nutrient for most life forms, however in excess it can be harmful. The ATP-driven copper pumps (Copper-ATPases) play critical role in living organisms by maintaining appropriate copper levels in cells and tissues. These evolutionary conserved polytopic membrane proteins are present in all phyla from simplest life forms (bacteria) to highly evolved eukaryotes (Homo sapiens). The presumed early function in metal detoxification remains the main function of Copper-ATPases in prokaryotic kingdom. In eukaryotes, in addition to removing excess copper from the cell, Copper-ATPases have another equally important function - to supply copper to copper dependent enzymes within the secretory pathway. This review focuses on the origin and diversification of Copper ATPases in eukaryotic organisms. From a single Copper ATPase in protozoans, a divergence into two functionally distinct ATPases is observed with the evolutionary appearance of chordates. Among the key functional domains of Copper-ATPases, the metal-binding N-terminal domain could be responsible for functional diversification of the copper ATPases during the course of evolution.     

Molecular Evolution of CXCR1, a G Protein-Coupled Receptor Involved in Signal Transduction of Neutrophils

Human neutrophils are a type of white blood cell, which forms an early line of defense against bacterial infections. Neutrophils are highly responsive to the chemokine, interleukin-8 (IL-8) due to the abundant distribution of CXCR1, one of the IL-8 receptors on the neutrophil cell surface. As a member of the GPCR family, CXCR1 plays a crucial role in the IL-8 signal transduction pathway in neutrophils. We sequenced the complete coding region of the CXCR1 gene in worldwide human populations and five representative nonhuman primate species. Our results indicate accelerated protein evolution in the human lineage, which was likely caused by Darwinian positive selection. The sliding window analysis and the codon-based neutrality test identified signatures of positive selection at the N-terminal ligand/receptor recognition domain of human CXCR1. [Reviewing Editor: Dr. Manyuan Long] The GenBank accession numbers of sequences reported herein are AY916760–AY916773.     

Molecular Cloning and Functional Characterization of Oxidosqualene Cyclases from Panax vietnamensis

Panax vietnamensis is a valuable medicinal resource with promising preclinical applications. Ginsenosides, which are triterpenoids, are the primary active components in P. vietnamensis. Oxidosqualene cyclases (OSCs) catalyze the formation of the basic skeleton of triterpenes from 2,3-oxidosqualene, which is a crucial step in the biosynthesis of triterpenoids. The OSCs involved in triterpenoid biosynthesis in P. vietnamensis have not yet been characterized. Four OSC genes (PvOSC1–4) were cloned from P. vietnamensis and functionally characterized via heterologous expression in yeast. Transgenic yeast expressing PvOSC1, PvOSC3, and PvOSC4 produced the corresponding products β-amyrin, cycloartenol, and dammarenediol-II, respectively. PvOSC1, PvOSC3, and PvOSC4 are monofunctional OSCs. In this study, we characterized three PvOSC genes, providing a better understanding of the biosynthesis of triterpenoids in P. vietnamensis and the multiple choices of plant OSCs for metabolic engineering in yeast and other hosts.     

Cloning of the y1 Locus of Maize,a Gene Involved in the Biosynthesis of Carotenoids

The y1 gene is one of the genes responsible for the production of [beta]-carotene in the endosperm and leaves of maize. We have cloned a Robertson's Mutator-tagged allele of the y1 gene (y1-mum) by using a Mu3 element as a hybridization probe. We substantiate that the cloned sequence is a portion of the y1 gene by molecular analyses of a revertant of a putative Mutator-induced y1 allele and the incidence of insertions within the cloned y1 sequence from several independently derived Mutator-induced y1 mutant stocks. The y1-mum sequence was used to isolate the standard Y1 allele, which conditions the presence of [beta]-carotene in the endosperm of the maize kernel.