Actin Phylogeny and Intron Distribution in Bangiophyte Red Algae(Rhodoplantae)

The molecular phylogeny of red algal actin genes, with emphasis on the paraphyletic “Bangiophyceae,” was examined and compared to the rhodophyte SSU rDNA phylogeny. Nineteen new genomic actin sequences and seven SSU rDNA sequences were obtained and subjected to diverse phylogenetic analyses (maximum likelihood, distance/neighbor-joining, maximum parsimony, Bayesian analyses, and, with respect to protein sequences, also quartet puzzling). The actin trees confirmed most of the major clades found in the SSU rDNA phylogenies, although with a lower resolution. An actin gene duplication in the florideophycean lineage is reported, presumably related to an increased complexity of sexual reproduction. In addition, the distribution and characteristics of spliceosomal introns found in some of the actin sequences were examined. Introns were found in almost all florideophycean actin genes, whereas only two bangiophyte sequences contained introns. One intron in the florideophycean actin genes was also found in metazoan, and, shifted by one or two nucleotides, in a glaucocystophyte, a cryptophyte, and two fungal actin genes, and thus may be an ancient intron.[Reviewing Editor: Dr. Yves Van de Peer]     

Gene Conversions May Obscure Actin Gene Family Relationships

Phylogenetic hypotheses of muscle actin evolution are significantly different when a sea urchin is used as a representative echinoderm than when a sea star is used. While sea urchin muscle actins support an echinoderm–chordate sister relationship, sea star sequences suggest that echinoderm muscle actins are convergent with chordate muscle actins. Our results suggest that gene conversion in the sea star muscle actin may be responsible for these discordant results. Received: 19 July 1999 / Accepted: 1 October 1999     

文昌鱼肌动蛋白基因家族的扩增(英文)

肌动蛋白是一种分布广泛而且在进化上十分保守的蛋白,是构成细胞骨架的关键组分.肌动蛋白通常被分成肌肉型和胞质型两种类型,各自行使着不同的功能.在此,作者对弗罗里达文昌鱼基因组中的肌动蛋白基因家族进行了系统分析,发现文昌鱼中该基因家族成员多达30多个,其中很多都是连锁分布的.基因结构趋于多样,分别包含2～7个外显子.进化分析的结果显示,文昌鱼的肌动蛋白基因家族可能通过串联重复而发生了扩增.作者还克隆了厦门文昌鱼两个不同的肌肉犁肌动蛋白基因,并比较了它们在文昌鱼早期胚胎中的表达图式.结果显示,这两个基因在表达上有着细微的差别,提示文昌鱼肌动蛋白基因家族成员在功能上的分化.上述结果将有助于阐明肌动蛋白基因家族及其功能在脊索动物中的演化.     

Structure and Evolution of the Actin Gene Family in Arabidopsis Thaliana

Higher plants contain families of actin-encoding genes that are divergent and differentially expressed. Progress in understanding the functions and evolution of plant actins has been hindered by the large size of the actin gene families. In this study, we characterized the structure and evolution of the actin gene family in Arabidopsis thaliana. DNA blot analyses with gene-specific probes suggested that all 10 of the Arabidopsis actin gene family members have been isolated and established that Arabidopsis has a much simpler actin gene family than other plants that have been examined. Phylogenetic analyses suggested that the Arabidopsis gene family contains at least two ancient classes of genes that diverged early in land plant evolution and may have separated vegetative from reproductive actins. Subsequent divergence produced a total of six distinct subclasses of actin, and five showed a distinct pattern of tissue specific expression. The concordance of expression patterns with the phylogenetic structure is discussed. These subclasses appear to be evolving independently, as no evidence of gene conversion was found. The Arabidopsis actin proteins have an unusually large number of nonconservative amino acid substitutions, which mapped to the surface of the actin molecule, and should effect protein-protein interactions.     

Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates

Vertebrate interferon-induced transmembrane (IFITM) genes have been demonstrated to have extensive and diverse functions, playing important roles in the evolution of vertebrates. Despite observance of their functionality, the evolutionary dynamics of this gene family are complex and currently unknown. Here, we performed detailed evolutionary analyses to unravel the evolutionary history of the vertebrate IFITM family. A total of 174 IFITM orthologous genes and 112 pseudogenes were identified from 27 vertebrate genome sequences. The vertebrate IFITM family can be divided into immunity-related IFITM (IR-IFITM), IFITM5 and IFITM10 sub-families in phylogeny, implying origins from three different progenitors. In general, vertebrate IFITM genes are located in two loci, one containing the IFITM10 gene, and the other locus containing IFITM5 and various numbers of IR-IFITM genes. Conservation of evolutionary synteny was observed in these IFITM genes. Significant functional divergence was detected among the three IFITM sub-families. No gene duplication or positive selection was found in IFITM5 sub-family, implying the functional conservation of IFITM5 in vertebrate evolution, which is involved in bone formation. No IFITM5 locus was identified in the marmoset genome, suggesting a potential association with the tiny size of this monkey. The IFITM10 sub-family was divided into two groups: aquatic and terrestrial types. Functional divergence was detected between the two groups, and five IFITM10-like genes from frog were dispersed into the two groups. Both gene duplication and positive selection were observed in aquatic vertebrate IFITM10-like genes, indicating that IFITM10 might be associated with the adaptation to aquatic environments. A large number of lineage- and species-specific gene duplications were observed in IR-IFITM sub-family and positive selection was detected in IR-IFITM of primates and rodents. Because primates have experienced a long history of viral infection, such rapid expansion and positive selection suggests that the evolution of primate IR-IFITM genes is associated with broad-spectrum antiviral activity.     

Signaling, Actin Dynamics and Endocytosis

Endocytosis is an essential process for normal function of all living cells. Cells get nutrients, and control the surface-expressional level of proteins as well as membrane hemostats through the endocytosis. Endocytosis process is regulated in response to functional status of a particular cell. Signaling events and the endocytosis process go hand in hand to fulfill cellular functions. Although our understanding of the endocytosis process has grown rapidly during the last decade, little is known about how it is interconnected functionally with the signaling status of cells. During endocytosis, vesicles are formed from the plasma membrane through complex molecular machinery. The location where the vesicles are formed is rich in cortical actin cytoskeleton that supports the plasma membrane. To enter cells, vesicles have to diffuse through the cortical actin cytoskeleton. The actin cytoskeleton has a very dynamic structure and actively participates a wide variety of cellular functions. In addition to its central role in cytokinesis, cell shape, cell motility, and cell polarity, a connection between the endocytosis process and the actin cytoskeleton has been implicated in both yeast and mammalian system. In recent years the knowledge on how the actin cytoskeleton participates in the generation of coordinated cellular responses to external stimuli is grown rapidly. In this review, we focus on the potential roles of the actin cytoskeleton in regulating the endocytosis process in response to signaling events.     

植物微丝骨架动态变化的调节

由球形肌动蛋白聚合而成的微丝骨架,又称肌动蛋白纤维,它在细胞运动、细胞形态建成以及物质运输等诸多生命活动中发挥重要作用。细胞内微丝的解聚和聚合动态特性是微丝骨架行使功能的重要基础,并受到如微丝结合蛋白、金属离子、小G蛋白等各种因素的严格控制。植物细胞微丝骨架的研究虽然晚于动物细胞,但也取得了飞速发展。本文对植物细胞内微丝骨架动态变化的作用机制及一些主要调节因子的最新研究进展做一介绍。     

Inhibitory Mechanism of FAT4 Gene Expression in Response to Actin Dynamics during Src-Induced Carcinogenesis

Oncogenic transformation is characterized by morphological changes resulting from alterations in actin dynamics and adhesive activities. Emerging evidence suggests that the protocadherin FAT4 acts as a tumor suppressor in humans, and reduced FAT4 gene expression has been reported in breast and lung cancers and melanoma. However, the mechanism controlling FAT4 gene expression is poorly understood. In this study, we show that transient activation of the Src oncoprotein represses FAT4 mRNA expression through actin depolymerization in the immortalized normal human mammary epithelial cell line MCF-10A. Src activation causes actin depolymerization via the MEK/Erk/Cofilin cascade. The MEK inhibitor U0126 blocks the inhibitory effect of Src on FAT4 mRNA expression and Src-induced actin depolymerization. To determine whether actin dynamics act on the regulation of FAT4 mRNA expression, we treated MCF-10A cells with the ROCK inhibitor Y-27632. Y-27632 treatment decreased FAT4 mRNA expression. This suppressive effect was blocked by siRNA-mediated knockdown of Cofilin1. Furthermore, simultaneous administration of Latrunculin A (an actin depolymerizing agent), Y-27632, and Cofilin1 siRNA to the cells resulted in a marked reduction of FAT4 mRNA expression. Intriguingly, we also found that FAT4 mRNA expression was reduced under both low cell density and low stiffness conditions, which suggests that mechanotransduction affects FAT4 mRNA expression. Additionally, we show that siRNA-mediated FAT4 knockdown induced the activity of the Hippo effector YAP/TAZ in MCF-10A cells. Taken together, our results reveal a novel inhibitory mechanism of FAT4 gene expression through actin depolymerization during Src-induced carcinogenesis in human breast cells.     

肌动蛋白和肌动蛋白基因的研究进展

细胞质来源肌动蛋白,构成细胞微丝,肌肉中的肌动蛋白主要是纤维形式即F－肌动蛋白。肌动蛋白基因编码序列是高度保守的,而非编码序列有较大的差异,反映其进化上的时间进程。对该基因的研究越来越受到重视,尤其在分子生物学中,常把它当作基因表达研究的参考标准。     

Structure and Dynamics of the Actin Filament

We used all-atom molecular dynamics simulations to investigate the structure and properties of the actin filament, starting with either the recent Oda model or the older Holmes model. Simulations of monomeric and polymerized actin show that polymerization changes the nucleotide-binding cleft, bringing together the Q137 side chain and bound ATP in a way that may enhance the ATP hydrolysis rate in the filament. Simulations with different bound nucleotides and conformations of the DNase I binding loop show that the persistence length of the filament depends only on loop conformation. Computational modeling reveals how bound phalloidin stiffens actin filaments and inhibits the release of γ-phosphate from ADP-P_i actin.     

Structural States and Dynamics of the D-Loop in Actin

Conformational changes induced by ATP hydrolysis on actin are involved in the regulation of complex actin networks. Previous structural and biochemical data implicate the DNase I binding loop (D-loop) of actin in such nucleotide-dependent changes. Here, we investigated the structural and conformational states of the D-loop (in solution) using cysteine scanning mutagenesis and site-directed labeling. The reactivity of D-loop cysteine mutants toward acrylodan and the mobility of spin labels on these mutants do not show patterns of an α-helical structure in monomeric and filamentous actin, irrespective of the bound nucleotide. Upon transition from monomeric to filamentous actin, acrylodan emission spectra and electron paramagnetic resonance line shapes of labeled mutants are blue-shifted and more immobilized, respectively, with the central residues (residues 43–47) showing the most drastic changes. Moreover, complex electron paramagnetic resonance line shapes of spin-labeled mutants suggest several conformational states of the D-loop. Together with a new (to our knowledge) actin crystal structure that reveals the D-loop in a unique hairpin conformation, our data suggest that the D-loop equilibrates in F-actin among different conformational states irrespective of the nucleotide state of actin.     

Sensing Actin Dynamics through Adherens Junctions

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Metabolism of delta-Aminolevulinic Acid in Red and Blue-Green Algae

δ-Aminolevulinic acid was incorporated in vivo into C-phycocyanin and B-phycoerythrin in two species of the Rhodophyta (Cyanidium caldarium, Porphyridium cruentum) and three species of the Cyanophyta (Anacystis nidulans, Plectonema boryanum, Phormidium luridum). Amino acid analysis of phycocyanin-¹⁴C from C. caldarium cells which had been incubated with δ-aminolevulinate-4-¹⁴C showed that 84% of the radioactivity incorporated was present in the phycocyanobilin chromophore and less than 16% of the radioactivity cochromatographed with amino acids. These results indicate that δ-aminolevulinate is utilized predominantly via the porphyrin pathway in C. caldarium. Conversely, analysis of phycocyanin-¹⁴C prepared from cells of A. nidulans, P. boryanum, and P. luridum which had been incubated with radiolabeled δ-aminolevulinate demonstrated that 85%, 81%, and 93%, respectively, of the radioactivity incorporated cochromatographed with amino acids. The ratio of incorporated radioactivity in amino acids and phycoerythrobilin was 40:60 in P. cruentum phycoerythrin obtained from cells which had been incubated with δ-aminolevulinate-4-¹⁴C. Succinate-2-3-¹⁴C appeared to be as good a carbon source of amino acids as did C₄ and C₅ of δ-aminolevulinate. These data demonstrate a major alternate route (other than the porphyrin pathway) of δ-aminolevulinate metabolism in red and blue-green algae. The factors responsible for the extent to which δ-aminolevulinate is utilized for synthesis of porphyrins and their derivatives and routes of δ-aminolevulinate catabolism in the organisms employed are discussed.     

Regulation of Actin Dynamics in Pollen Tubes: Control of Actin Polymer Level

Actin cytoskeleton undergoes rapid reorganization in response to internal and external cues. How the dynamics of actin cytoskeleton are regulated, and how its dynamics relate to its function are fundamental questions in plant cell biology. The pollen tube is a well characterized actin-based cell morphogenesis in plants. One of the striking features of actin cytoskeleton characterized in the pollen tube is its surprisingly low level of actin polymer. This special phenomenon might relate to the function of actin cytoskeleton in pollen tubes. Understanding the molecular mechanism underlying this special phenomenon requires careful analysis of actin-binding proteins that modulate actin dynamics directly. Recent biochemical and biophysical analyses of several highly conserved plant actin-binding proteins reveal unusual and unexpected properties, which emphasizes the importance of carefully analyzing their action mechanism and cellular activity. In this review, we highlight an actin monomer sequestering protein, a barbed end capping protein and an F-actin severing and dynamizing protein in plant. We propose that these proteins function in harmony to regulate actin dynamics and maintain the low level of actin polymer in pollen tubes.     

Photoinhibition of Photosynthesis and its Recovery in Red Algae

In different marine red algae (Chondrus crispus, Delesseria sanguinea, Membranoptera alata, Phycodrys rubens, Phyllophora truncata, Polyneura hilliae) photoinhibition of photosynthesis has been investigated by means of both fluorescence and oxygen measurements. Measurements of absolute oxygen production show that photoinhibition causes a decline in the initial slope and in the rate of bending of the fluence rate-response curve (i.e. the photosynthetic efficiency at non-saturating fluence rates), as well as a decline in the photosynthetic capacity (Pm) at saturating fluence rates. Fluorescence data (Fv/Fm) were consistent with the results of oxygen measurements. Under excessive light photoinhibition protects photosynthesis against photo-damage in red algae. However, an increase in the initial fluorescence (Fo) after photoinhibitory treatment indicates that it could not prevent photodamage entirely. Action spectra of photoinhibition demonstrate that the main photoinhibition site in Polyneura hiliae is PS II, because far red light absorbed by PS I was ineffective. The strong increase of Fo in the blue wavelength range and the slight and partial recovery in weak blue light indicate that blue light especially causes photodamage. Recovery of photosynthesis requires dim white light conditions. Experiments with monochromatic light also show a wavelength dependence of recovery. Moreover, the recovery of photosynthesis after a photoinhibitory treatment is strongly temperature dependent, indicating participation of enzymatic processes. The comparison of fluorescence and oxygen measurement of the recovery shows different results in some species. The rate of oxygen production in red control light increased immediately after photoinhibited algae were exposed to weak light conditions. Surprisingly, the ratio of variable to maximum fluorescence (Fv/Fm) of Phyllophora truncata and the maximum fluorescence (Fm) of Polyneura hilliae show first a delay of the recovery under weak light conditions. Thus, in recovery experiments fluorescence and oxygen data are not quite consistent.