The Molecular Evolution of the Small Heat-Shock Proteins in Plants

The small heat-shock proteins have undergone a tremendous diversification in plants; whereas only a single small heat-shock protein is found in fungi and many animals, over 20 different small heat-shock proteins are found in higher plants. The small heat-shock proteins in plants have diversified in both sequence and cellular localization and are encoded by at least five gene families. In this study, 44 small heat-shock protein DNA and amino acid sequences were examined, using both phylogenetic analysis and analysis of nucleotide substitution patterns to elucidate the evolutionary history of the small heat-shock proteins. The phylogenetic relationships of the small heat-shock proteins, estimated using parsimony and distance methods, reveal that gene duplication, sequence divergence and gene conversion have all played a role in the evolution of the small heat-shock proteins. Analysis of nonsynonymous substitutions and conservative and radical replacement substitutions (in relation to hydrophobicity) indicates that the small heat-shock protein gene families are evolving at different rates. This suggests that the small heat-shock proteins may have diversified in function as well as in sequence and cellular localization.     

Molecular Evolution of the Plant Virus Family Bromoviridae Based on RNA3-Encoded Proteins

We have carried out an evolutionary study of the two proteins encoded by the RNA 3 from members of the plant virus family Bromoviridae. Using maximum likelihood methods, we have inferred the patterns of amino acid substitution that better explain the diversification of this viral family. The results indicate that the molecular evolution of this family was rather complex, with each protein evolving at different rates and according to different patterns of amino acid substitution. These differences include different amino acid equilibrium frequencies, heterogeneity in substitution rates among sites, and covariation among sites. Despite these differences, the model of protein evolution that better fits both proteins is one specifically proposed for the evolution of globular proteins. We also found evidence for coevolution between domains of these two proteins. Finally, our analyses suggest that the molecular clock hypothesis does not hold, since different lineages evolved at different rates. The implications of these results for the taxonomy of this important family of plant viruses are discussed. [Reviewing Editor: Dr. Martin Kreitman and Dr. James Bull]     

Molecular Evolution of the Myeloperoxidase Family

Animal myeloperoxidase and its relatives constitute a diverse protein family, which includes myeloperoxidase, eosinophil peroxidase, thyroid peroxidase, salivary peroxidase, lactoperoxidase, ovoperoxidase, peroxidasin, peroxinectin, cyclooxygenase, and others. The members of this protein family share a catalytic domain of about 500 amino acid residues in length, although some members have distinctive mosaic structures. To investigate the evolution of the protein family, we performed a comparative analysis of its members, using the amino acid sequences and the coordinate data available today. The results obtained in this study are as follows: (1) 60 amino acid sequences belonging to this family were collected by database searching. We found a new member of the myeloperoxidase family derived from a bacterium. This is the first report of a bacterial member of this family. (2) An unrooted phylogenetic tree of the family was constructed according to the alignment. Considering the branching pattern in the obtained phylogenetic tree, together with the mosaic features in the primary structures, 60 members of the myeloperoxidase family were classified into 16 subfamilies. (3) We found two molecular features that distinguish cyclooxygenase from the other members of the protein family. (4) Several structurally deviated segments were identified by a structural comparison between cyclooxygenase and myeloperoxidase. Some of the segments seemed to be associated with the functional and/or structural differences between the enzymes. Received: 25 January 2000 / Accepted: 19 July 2000     

The Family of Major Royal Jelly Proteins and Its Evolution

A cDNA encoding a new member of the gene family of major royal jelly proteins (MRJPs) from the honeybee, Apis mellifera, was isolated and sequenced. Royal jelly (RJ) is a secretion of the cephalic glands of nurse bees. The origin and biological function of the protein component (12.5%, w/w) of RJ is unknown. We show that the MRJP gene family encodes a group of closely related proteins that share a common evolutionary origin with the yellow protein of Drosophila melanogaster. Yellow protein functions in cuticle pigmentation in D. melanogaster. The MRJPs appear to have evolved a novel nutritional function in the honeybee. Received: 26 September 1998 / Accepted: 28 February 1999     

Molecular Characterization and Evolution of the SPRR Family of Keratinocyte Differentiation Markers Encoding Small Proline-Rich Proteins

SPRR genes (formerly SPR) encode a novel class of polypeptides (small pr oline rich proteins) that are strongly induced during differentiation of human epidermal keratinocytes in vitro and in vivo. Recently we found that the N- and C-terminal domains of these proteins show strong sequence homology to loricrin and involucrin, suggesting that SPRR proteins constitute a new class of cornified envelope precursor proteins. Here we show that SPRR proteins are encoded by closely related members of a gene family, consisting of two genes for SPRR1, approximately seven genes for SPRR2, and a single gene for SPRR3. All SPRR genes are closely linked within a 300-kb DNA segment on human chromosome 1 band q21-q22, a region where the related loricrin and involucrin genes have also been mapped. The most characteristic feature of the SPRR gene family resides in the structure of the central segments of the encoded polypeptides that are built up from tandemly repeated units of either eight (SPRR1 and SPRR3) or nine (SPRR2) amino acids with the general consensus *K*PEP**. Sequencing data of the different members, together with their clustered chromosomal organization, strongly suggest that this gene family has evolved from a single progenitor gene by multiple intra- and intergenic duplications. Analysis of the different SPRR subfamilies reveals a gene-specific bias to either intra- or intergenic duplication. We propose that a process of homogenization has acted on the different members of one subfamily, whereas the different subfamilies appear to have diverged from each other, at the levels of both protein structure and gene regulation.     

Sexual Selection and the Molecular Evolution of ADAM Proteins

Rapid evolution has been identified for many reproductive genes and recent studies have combined phylogenetic tests and information on species mating systems to test sexual selection. Here we examined the molecular evolution of the ADAM gene family, a diverse group of 35 proteins capable of adhesion to and cleavage of other proteins, using sequence data from 25 mammalian genes. Out of the 25 genes analyzed, all those expressed in male reproductive tissue showed evidence of positive selection. Positively selected amino acids within the protein adhesion domain were only found in sperm surface ADAM proteins (ADAMs 1, 2, 3, 4, and 32) suggesting selection driven by male × female interactions. We tested heterogeneity in rates of evolution of the adhesion domain of ADAM proteins by using sequence data from Hominidae and macaques. The use of the branch and branch-site models (PAML) showed evidence of higher d _N/d _S and/or positive selection linked to branches experiencing high postmating selective pressures (chimpanzee and macaque) for Adams 2, 18, and 23. Moreover, we found consistent higher proportion of nonsynonymous relative to synonymous and noncoding sequence substitutions in chimpanzee and/or macaque only for Adams 2, 18, and 23. Our results suggest that lineage-specific sexual selection bouts might have driven the evolution of the adhesion sperm protein surface domains of ADAMs 2 and 18 in primates. Adams 2 and 18 are localized in chromosome 8 of primates and adjacent to each other, so their evolution might have also been influenced by their common genome localization.     

软体动物粗蛋白对藻类的凝集作用

采用绿色巴夫藻（Pavlova viridis)、盐藻（Dunaliella salina)、塔胞藻（Pyramimonas sp.)、海产小球藻（Chlorella vulgaris)、亚心型扁藻（Pyatymonas cordiformis)、蛋白核小球藻（Chlorella pyrenoidosa)、紫球藻（Porphyridium purpureum)等7种单细胞藻类对福建省10种常见软体动物粗蛋白提取物进行凝集活性筛选,其中有7种动物粗蛋白显示出对藻类细胞有凝集活性。同时,发现紫球藻的敏感性强于其他种类。这些粗蛋白的凝集活性在不同酸碱度和高温下表现出较强的稳定性,尤其是薄壳绿螂、菲律宾蛤仔、斑玉螺、短蛸的粗蛋白在95℃恒温15min后仍有活性。这些动物粗蛋白对紫球藻的凝集活性可以被0.02mol/L和0.04mol/L的EDTA所抑制,同时还能为9种糖类所抑制。     

啮齿目泌乳刺激素基因家族的分子进化研究

在大鼠基因组数据库中搜索得到两个泌乳刺激素基因家族的新成员。进一步分析显示该基因家族起源于啮齿目和其他哺乳动物分歧之后,而且大部分基因座位的重排在大、小鼠分歧之前已经完成。但PL-Ⅰ和PL-Ⅱ基因簇却是例外,它们在基因树上以物种特异的方式聚类。结合基因转换的检验、染色体上相对位置比较和基因重复时间估计的结果,认为啮齿目PL-Ⅰ和PL-Ⅱ基因是物种特异的,它们由一系列在大、小鼠分歧之后发生的基因重复事件形成。结果还揭示了在啮齿目泌乳刺激素基因家族进化过程中持续不断的发生了基因重复和基因分化事件。     

Molecular Evolution of Miraculin-Like Proteins in Soybean Kunitz Super-Family

Miraculin-like proteins (MLPs) belong to soybean Kunitz super-family and have been characterized from many plant families like Rutaceae, Solanaceae, Rubiaceae, etc. Many of them possess trypsin inhibitory activity and are involved in plant defense. MLPs exhibit significant sequence identity (~30-95%) to native miraculin protein, also belonging to Kunitz super-family compared with a typical Kunitz family member (~30%). The sequence and structure-function comparison of MLPs with that of a classical Kunitz inhibitor have demonstrated that MLPs have evolved to form a distinct group within Kunitz super-family. Sequence analysis of new genes along with available MLP sequences in the literature revealed three major groups for these proteins. A significant feature of Rutaceae MLP type 2 sequences is the presence of phosphorylation motif. Subtle changes are seen in putative reactive loop residues among different MLPs suggesting altered specificities to specific proteases. In phylogenetic analysis, Rutaceae MLP type 1 and type 2 proteins clustered together on separate branches, whereas native miraculin along with other MLPs formed distinct clusters. Site-specific positive Darwinian selection was observed at many sites in both the groups of Rutaceae MLP sequences with most of the residues undergoing positive selection located in loop regions. The results demonstrate the sequence and thereby the structure-function divergence of MLPs as a distinct group within soybean Kunitz super-family due to biotic and abiotic stresses of local environment.     

Molecular Evolution of Prolactin Gene Family in Rodents

In this study, we identified two novel members of prolactin gene family in rat by blast searches against the published genomic database. A further analysis showed that gene duplications leading to PRL gene family in rodents occurred after rodents diverged from other mammals. Major reorganization of the gene loci in rodents was largely completed before the split of rat and mouse. But PL-I and PL-II genes are the exceptions, which have clustered in a species-specific manner in the phylogenetic tree. By combining results from gene conversion testing, relative chromosomal location comparison and estimated time for gene duplication, we believe that rodent PL-I and PL-II genes are species-specific and are the results of serial duplications which occurred after the divergence of mouse and rat. Our analysis also reveals that continual gene duplication and divergence occurred during the evolution of rodent PRL gene family.     

miR-34基因家族的分子进化

根据miRNA基因在进化中高度保守的特点,利用生物信息学方法在目前已测序的动物物种中搜寻参与哺乳动物早期发育调控的mir-34基因的同源序列,在33个不同的动物物种中获得了miR-34基因的54条同源序列,其中18条为新发现的序列。表明miR-34是高度保守的,广泛存在于后生动物中。目前发现的mir-34基因80%位于基因间隔区,少数位于蛋白编码基因的内含子区和3′UTR上。不同动物中,mir-34基因成熟序列的同源性为68%,前体序列为38.89%。在无脊椎动物中只有一个mir-34,而在几乎所有的脊椎动物中都有mir-34a,mir-34b,mir-34c,形成miR-34基因家族。系统进化分析表明,脊椎动物中miR-34基因家族是通过基因的串联和局部重复形成的,这个过程中伴随着个别碱基的变异。     

Molecular Evolution of the Plant R Regulatory Gene Family

Anthocyanin pigmentation patterns in different plant species are controlled in part by members of the myc-like R regulatory gene family. We have examined the molecular evolution of this gene family in seven plant species. Three regions of the R protein show sequence conservation between monocot and dicot R genes. These regions encode the basic helix-loop-helix domain, as well as conserved N-terminal and C-terminal domains; mean replacement rates for these conserved regions are 1.02 X 10(-9) nonsynonymous nucleotide substitutions per site per year. More than one-half of the protein, however, is diverging rapidly, with nonsynonymous substitution rates of 4.08 X 10(-9) substitutions per site per year. Detailed analysis of R homologs within the grasses (Poaceae) confirm that these variable regions are indeed evolving faster than the flanking conserved domains. Both nucleotide substitutions and small insertion/deletions contribute to the diversification of the variable regions within these regulatory genes. These results demonstrate that large tracts of sequence in these regulatory loci are evolving at a fairly rapid rate.     

载脂蛋白多基因家族分子进化的研究

与脂质运输有关的载脂蛋白基因构成一个复杂的多基因家族。为探讨这种演化时间长的基因家族的进化规律,本文首先建立了一种在非均衡进化速率条件下计算系统发生树中任意分支长度的简易方法,并可在此基础上算出无根分支系统树中分歧年代的期望值。进一步对本文科１０个种属共２６种载脂蛋白的系统演作作了实际分析,结果提示：①ＡｐｏＡ－Ｉ＇ＡｐｏＡ－ＩＶ,ＡｐｏＥ及ＡｐｏＡ－ＩＩ的共同祖先可能在奥陶纪水生脊椎动物中就已存     

Molecular Evolution of Viral Multifunctional Proteins: The Case of Potyvirus HC-Pro

Our knowledge on the mode of evolution of the multifunctional viral proteins remains incomplete. To tackle this problem, here, we have investigated the evolutionary dynamics of the potyvirus multifunctional protein HC-Pro, with particular focus on its functional domains. The protein was partitioned into the three previously described functional domains, and each domain was analyzed separately and assembled. We searched for signatures of adaptive evolution and evolutionary dependencies of amino acid sites within and between the three domains using the entire set of available potyvirus sequences in GenBank. Interestingly, we identified strongly significant patterns of co-occurrence of adaptive events along the phylogenetic tree in the three domains. These patterns suggest that Domain I, whose main function is to mediate aphid transmission, has likely been coevolving with the other two domains, which are involved in different functions but all requiring the capacity to bind RNA. By contrast, episodes of positive selection on Domains II and III did not correlate, reflecting a trade-off between their evolvability and their evolutionary dependency likely resulting from their functional overlap. Covariation analyses have identified several groups of amino acids with evidence of concerted variation within each domain, but interdomain significant covariations were only found for Domains II and III, further reflecting their functional overlapping.     

Molecular Functions of Oxygen-Evolving Complex Family Proteins in Photosynthetic Electron Flow

Oxygen-evolving complex (OEC) protein is the original name for membrane-peripheral subunits of photosystem (PS) Ⅱ. Recently,multiple isoforms and homologs for OEC proteins have been identified in the chloroplast thylakoid lumen, indicating that functional diversification has occurred in the OEC family. Gene expression profiles suggest that the Arabidopsis OEC proteins are roughly categorized into three groups: the authentic OEC group, the stressresponsive group, and the group including proteins related to the chloroplast NAD(P)H dehydrogenase (NDH) complex involved in cyclic electron transport around PSI. Based on the above gene expression profiles, molecular functions of the OEC family proteins are discussed together with our current knowledge about their functions.     

WASP Family Proteins: Their Evolution and Its Physiological Implications

WASP family proteins control actin polymerization by activating the Arp2/3 complex. Several subfamilies exist, but their regulation and physiological roles are not well understood, nor is it even known if all subfamilies have been identified. Our extensive search reveals few novel WASP family proteins. The WASP, WASH, and SCAR/WAVE subfamilies are evolutionarily ancient, with WASH the most universally present, whereas WHAMM/JMY first appears in invertebrates. An unusual Dictyostelium WASP homologue that has lost the WH1 domain has retained its function in clathrin-mediated endocytosis, demonstrating that WASPs can function with a remarkably diverse domain topology. The WASH and SCAR/WAVE regulatory complexes are much more rigidly maintained; their domain topology is highly conserved, and all subunits are present or lost together, showing that the complexes are ancient and functionally interdependent. Finally, each subfamily has a distinctive C motif, indicating that this motif plays a specific role in each subfamily''s function, unlike the generic V and A motifs. Our analysis identifies which features are universally conserved, and thus essential, and which are branch-specific modifications. It also shows the WASP family is more widespread and diverse than currently appreciated and unexpectedly biases the physiological role of the Arp2/3 complex toward vesicle traffic.     

Molecular Evolution of Hemojuvelin and the Repulsive Guidance Molecule Family

Repulsive guidance molecules (RGMs) are found in vertebrates and chordates and are involved in embryonic development and iron homeostasis. Members of this family are GPI-linked membrane proteins that contain an N-terminal signal peptide, a C-terminal propeptide, and a conserved RGD motif. Vertebrates are known to possess three paralogues; RGMA and RGMB (sometimes called Dragon) are expressed in the nervous system and are thought to play various roles in neural development. Hemojuvelin (HJV; also called repulsive guidance molecule c, RGMC) is the third member of this family, and mutations in this gene result in a form of juvenile hemochromatosis (type 2A). Phylogenetic analyses of 55 different RGM family sequences from 21 different species support the existence of a novel gene, found only in fish, which we have labeled RGMD. The pattern of conserved residues in each family identifies new candidates for important functional roles, including ligand binding. [Reviewing Editor: Dr. Gail Simmons]     

Molecular Phylogeny and Evolution of the Plant-Specific Seven-Transmembrane MLO Family

Abstract Homologues of barley Mlo encode the only family of seven-transmembrane (TM) proteins in plants. Their topology, subcellular localization, and sequence diversification are reminiscent of those of G-protein coupled receptors (GPCRs) from animals and fungi. We present a computational analysis of MLO family members based on 31 full-size and 3 partial sequences, which originate from several monocot species, the dicot Arabidopsis thaliana, and the moss Ceratodon purpureus. This enabled us to date the origin of the Mlo gene family back at least to the early stages of land plant evolution. The genomic organization of the corresponding genes supports a monophyletic origin of the Mlo gene family. Phylogenetic analysis revealed five clades, of which three contain both monocot and dicot members, while two indicate class-specific diversification. Analysis of the ratio of nonsynonymous-to-synonymous changes in coding sequences provided evidence for functional constraint on the evolution of the DNA sequences and purifying selection, which appears to be reduced in the first extracellular loop of 12 closely related orthologues. The 31 full-size sequences were examined for potential domain-specific intramolecular coevolution. This revealed evidence for concerted evolution of all three cytoplasmic domains with each other and the C-terminal cytoplasmic tail, suggesting interplay of all intracellular domains for MLO function.     

促葡萄糖转运蛋白基因家族的分子进化研究

葡萄糖转运蛋白是一个在结构上相似功能上不同的多基因家族（ＧＬＵＴ１－ＧＬＵＴ５）。由于这一组蛋白和体内的葡萄糖利用有关,因此被认为是糖尿病胰岛素抵抗（抗性）的一个候选基因。本文比较了不同种生物这一基因家族的氨基酸和核苷酸顺序;推测了亲水性和疏水性分布;计算了蛋白质和核苷酸的进化距离,并在此基础上构建了分子进化树。研究表明：这一基因家族具有高度的同源性、极为相似的亲水性和疏水性分布以及结构的对称性。提示这一基因家族起源于一个共同的祖先并可能通过基因的重复而形成。这一进化机制可能有利于氨基酸结构的稳定及抵抗突变的作用。由于邻元法构建的进化树其分支长度存在差异,提示在这一基因家族的进化过程中,各分支上的进化速率并不相同。蛋白质进化距离和核苷酸进化距离所构建进化树的差异提示了在基因组中可能存在隐匿替换。两种方法构建的进化树都提示了ＧＬＵＴ１、３、４在结构和功能上要更为保守。