Conserved DNA Motifs,Including the CENP-B Box-like,Are Possible Promoters of Satellite DNA Array Rearrangements in Nematodes

Tandemly arrayed non-coding sequences or satellite DNAs (satDNAs) are rapidly evolving segments of eukaryotic genomes, including the centromere, and may raise a genetic barrier that leads to speciation. However, determinants and mechanisms of satDNA sequence dynamics are only partially understood. Sequence analyses of a library of five satDNAs common to the root-knot nematodes Meloidogyne chitwoodi and M. fallax together with a satDNA, which is specific for M. chitwoodi only revealed low sequence identity (32–64%) among them. However, despite sequence differences, two conserved motifs were recovered. One of them turned out to be highly similar to the CENP-B box of human alpha satDNA, identical in 10–12 out of 17 nucleotides. In addition, organization of nematode satDNAs was comparable to that found in alpha satDNA of human and primates, characterized by monomers concurrently arranged in simple and higher-order repeat (HOR) arrays. In contrast to alpha satDNA, phylogenetic clustering of nematode satDNA monomers extracted either from simple or from HOR array indicated frequent shuffling between these two organizational forms. Comparison of homogeneous simple arrays and complex HORs composed of different satDNAs, enabled, for the first time, the identification of conserved motifs as obligatory components of monomer junctions. This observation highlights the role of short motifs in rearrangements, even among highly divergent sequences. Two mechanisms are proposed to be involved in this process, i.e., putative transposition-related cut-and-paste insertions and/or illegitimate recombination. Possibility for involvement of the nematode CENP-B box-like sequence in the transposition-related mechanism and together with previously established similarity of the human CENP-B protein and pogo-like transposases implicate a novel role of the CENP-B box and related sequence motifs in addition to the known function in centromere protein binding.     

Specificity of SAF-A and lamin B binding in vitro correlates with the satellite DNA bending state

There is evidence that Matrix Attachment Region (MAR)-binding proteins also bind satellite DNA (satDNA). The aim of the current work was to determine whether the major nuclear matrix (NM) MAR-binding proteins are able to recognize satDNAs of different locations and what DNA structural features are important for the recognition. In nuclei and NM, a number of the same polypeptides were recognized on a southwestern blot when MAR of immunoglobulin kappa gene (Ig kappa MAR) and pericentromeric (periCEN) satDNA fragments were used. However, the binding decreased dramatically when human and mouse CEN satDNA were used for the probes. After an NM extract was subjected to ion exchange chromatography, the main DNA-binding proteins were identified as SAF-A (scaffold attachment factor A) and lamin B. It was not possible to test the binding of lamin B by gel mobility shift assay (GMSA), but SAF-A showed an ability to distinguish CEN and periCEN satDNA fragments in GMSA. While periCEN fragments have an abnormally slow mobility on electrophoresis, which is a hallmark of bent DNA, CEN satDNA fragments have a normal mobility. A computer analysis was done using the wedge model (Ulanovsky and Trifonov [1987] Nature 326:720-722), which describes how the curved state depends on particular nucleotide sequences. The curved states of the fragments predicted by the model are in good agreement with their ability to be recognized by NM proteins. Thus SAF-A and lamin B are able to recognize conserved structural features of satDNA in the same way that MAR-binding proteins recognize MARs in spite of a lack of a consensus sequence. CEN and periCEN satDNAs are distinguished by proteins in correlation with the helical curvature of these fragments.     

Satellite DNA content illuminates the ancestry of a supernumerary (B) chromosome

B chromosomes are supernumerary genomic elements most likely derived from the standard (A) chromosomes, whose dispensability has freed their DNA sequences to evolve fast, thus making it difficult to uncover their ancestry. Here, we show the ancestry of a B chromosome in the grasshopper Eumigus monticola by means of the high-throughput analysis of the satellitome, i.e., the whole collection of satellite DNA (satDNA). The satellitome found in this species consists of 27 satDNA families, with monomer length between 5 and 325 nt and A + T content between 42.9 and 83.3 %. Two out of the 20 clustered satDNA families (EmoSat26–41 and EmoSat27–102) were observed only on the B chromosome. The A chromosome carrying the highest number of satDNA families was the megameric S8 (13 families), six of which were also present in the B chromosome, and three of these were exclusive of the S8 and B chromosomes. The absence in the B chromosome of the H3 histone gene cluster (located interstitially on S8) and three satDNA families (located distally on S8) allowed delimiting the possible origin of the B chromosome to the proximal third of the S8 autosome, through a breakpoint between EmoSat11–122 and the H3 cluster. Interestingly, bioinformatic analysis revealed the presence of seeds for the two B-specific satDNAs in the A chromosomes, suggesting their massive amplification in the B chromosome after its origin. Therefore, intraspecifically arisen B chromosomes can harbor DNA sequences apparently being B-specific.     

Chromosomal localization and evolution of satellite DNAs and heterochromatin in grasses (Poaceae), especially tribe Aveneae

The physical mapping of three abundant tandemly repeated DNA sequences, CON1, CON2, and COM2, and the distributional pattern of AT- and GC-rich regions in the chromosomes of 32 species of the grass family Poaceae have been established by means of fluorescence in situ hybridization and fluorochrome banding with chromomycin and DAPI. Additionally, locations of 5S, 35S rDNA, and the C-banding pattern were examined. All satellite DNAs (satDNA) tested are situated predominantly subtelomerically in the chromosomes, but occur also colocalized with 35S and 5S ribosomal DNAs (rDNA). Especially, CON2 is most often colocalized with the 5S rDNA, but is evolutionarily not derived from it. Subtelomeric heterochromatin bands are frequently, but not always correlated with satDNA bands. Moreover, the DAPI- or rarely chromomycin-positive stainability of heterochromatin is not caused by these satDNAs as revealed by their sequence organization, showing too few clusters of AT or GC base pairs as required for binding of the fluorochromes. The occurrence of satDNAs is not correlated with that of other components of the heterochromatin. Proportions of satDNAs and other sequences of the heterochromatin relative to the entire genome appear subjected to a much faster evolutionary change than the rather stable proportions of the rDNAs. Heteromorphism in banding patterns found in many species is related in most instances with breeding system and life form. The independent evolution and amplification of different satDNAs is discussed in relation to molecular phylogenetic data. The value and limitations of satDNA data in addressing systematic questions in grasses is exemplified for several grass subfamilies and tribes.     

Variability of satellite DNA in 2 groups of field mice (Rodentia, Microtinae)

Nuclear DNAs of three forms of Microtus juldashi--M. carruthersi (group 1) and of three subspecies of polytypic species Alticola macrotis (group 2) were compared. Intensive interpopulational karyotype differentiation was observed in both groups, particularly, for centromeric heterochromatin quantity and localization. As satellite DNAs (satDNAs) were present in C-heterochromatin of the Rodents groups studied, the latter were used as a model for comparison of the satDNAs in the species in statu nascendi. With this view, the nuclear DNAs were studied by means of the neutral CsCl equilibrium centrifugation. In both groups examined, no correlation was found between the presence, the characteristics of the satDNAs and morphological as well as cytogenetic features of the animals. These results are an indirect confirmation of the idea, according to which satDNA does not possibly play significant role in the development of the reproductive isolation and species formation.     

Molecular evolution of the pDo500 satellite DNA family in Dolichopoda cave crickets (Rhaphidophoridae)

Background  

Non-coding satellite DNA (satDNA) usually has a high turn-over rate frequently leading to species specific patterns. However, some satDNA families evolve more slowly and can be found in several related species. Here, we analyzed the mode of evolution of the pDo500 satDNA family of Dolichopoda cave crickets. In addition, we discuss the potential of slowly evolving satDNAs as phylogenetic markers.     

昆虫表皮蛋白基因研究进展

在昆虫表皮的发生、分化和昆虫躯体外部重要部位及器官的构建中,表皮蛋白是不可或缺的组成元素。本文在简要总结了目前昆虫表皮蛋白鉴定与分类方面研究的基础上,重点对近10年来昆虫表皮蛋白基因的时空表达模式、激素及转录因子对表皮蛋白基因表达的调控、表皮蛋白基因功能的研究进展进行了综述,探讨了其在害虫防治中可能的应用前景,旨在为进一步研究昆虫表皮蛋白基因及其潜在利用价值提供参考。目前报道的昆虫表皮蛋白序列已超过1 400条,分为12个家族,如CPR, CPF, CPFL和Tweedle等。经由蜕皮激素激活的相关转录因子（如βFTZ-F1和BR-C等）作用于表皮蛋白基因上游的顺式作用元件,开启或关闭基因,以调控表皮蛋白基因的表达。表皮蛋白基因在昆虫表皮整合,体形塑造,活动能力,抗逆与抗药性,以及先天免疫等生理现象和生理过程中有不可或缺的作用。因此,如果能够通过抑制关键表皮蛋白基因的表达,或将其从基因组中删除,以阻碍昆虫的发育或扰乱昆虫的繁殖能力,或可为害虫防治策略提供参考。     

Plant highly repeated satellite DNA: Molecular evolution,distribution and use for identification of hybrids

Relationships among genomes are often revealed by the occurrence of common or related satellite DNA (satDNA) types. A typical satDNA characterized by specific sites for one (or more) restriction endonuclease(s) is called ‘restriction satellite DNA’. Restriction satDNA comprises ‐ in addition to transposons and retrotransposable elements ‐ often highly repeated genome components present in most higher plants. Large arrays of satDNA elements are concentrated at subtelo‐meric and/or centromeric regions (intermingled with other retrotransposon‐derived elements), however, they can be also located as large intercalating blocks along the chromosome. The head‐to‐tail tandemly arranged repeat units (monomers) of satDNA mostly exhibit lengths of 160 to 180 bp or 320 to 370 bp, but other lengths were also found in plants. In particular, in interspecific hybrids between more distantly related species, which often exist only after polyploidization, the individual repetitive DNA of the crossing partners contribute to recombination and rearrangement processes in the hybrids, thereby stimulating genome evolution. Here, we concentrate on the possible origin, molecular evolution, organization and distribution of highly repeated satDNA in various higher plants with emphasis on hybrids and allopolyploids.     

A hypothesis to account for the selective and diverse actions of neonicotinoid insecticides at their molecular targets,nicotinic acetylcholine receptors: catch and release in hydrogen bond networks

The low mammalian toxicity of neonicotinoid insecticides has been shown to be attributable, at least in part, to their selective actions on insect nicotinic acetylcholine receptors (nAChRs). There are multiple nAChRs in insects and a wealth of neonicotinoid chemicals. Studies to date have discribed a wide range of effects on nAChRs, notably partial agonist, super agonist and antagonist actions. Both the diversity of the neonicotinoid actions and their selectivity for insect over vertebrate nAChRs are the result of physicochemical and steric interactions at their molecular targets (nAChRs). In such interactions, the formation and breakage of hydrogen bond (HB) networks plays a key role. Therefore the loss or gain of even a single HB resulting from either structural changes in neonicotinoids, or the amino acid sequence of a particular nAChR subunit, could result in a drastic modification of neonicotinoid actions. In addition to the amino acid residues, the backbone carbonyl of nAChRs may also be involved in the formation of HB networks with neonicotinoids.     

Interplay of selective pressure and stochastic events directs evolution of the MEL172 satellite DNA library in root-knot nematodes

According to the library model, related species can have in common satellite DNA (satDNA) families amplified in differing abundances, but reasons for persistence of particular sequences in the library during long periods of time are poorly understood. In this paper, we characterize 3 related satDNAs coexisting in the form of a library in mitotic parthenogenetic root-knot nematodes of the genus Meloidogyne. Due to sequence similarity and conserved monomer length of 172 bp, this group of satDNAs is named MEL172. Analysis of sequence variability patterns among monomers of the 3 MEL172 satellites revealed 2 low-variable (LV) domains highly reluctant to sequence changes, 2 moderately variable (MV) domains characterized by limited number of mutations, and 1 highly variable (HV) domain. The latter domain is prone to rapid spread and homogenization of changes. Comparison of the 3 MEL172 consensus sequences shows that the LV domains have 6% changed nucleotide positions, the MV domains have 48%, whereas 78% divergence is concentrated in the HV domain. Conserved distribution of intersatellite variability might indicate a complex pattern of interactions in heterochromatin, which limits the range and phasing of allowed changes, implying a possible selection imposed on monomer sequences. The lack of fixed species-diagnostic mutations in each of the examined MEL172 satellites suggests that they existed in unaltered form in a common ancestor of extant species. Consequently, the evolution of these satellites seems to be driven by interplay of selective constraints and stochastic events. We propose that new satellites were derived from an ancestral progenitor sequence by nonrandom accumulation of mutations due to selective pressure on particular sequence segments. In the library of particular taxa, established satellites might be subject to differential amplification at chance due to stochastic mechanisms of concerted evolution.     

Accumulation of Y-specific satellite DNAs during the evolution of <Emphasis Type="Italic">Rumex acetosa</Emphasis> sex chromosomes

The study of the molecular structure of young heteromorphic sex chromosomes of plants has shed light on the evolutionary forces that control the differentiation of the X and Y during the earlier stages of their evolution. We have used the model plant Rumex acetosa, a dioecious species with multiple sex chromosomes, 2n = 12 + XX female and 2n = 12 + XY₁Y₂ male, to analyse the significance of repetitive DNA accumulation during the differentiation of the Y. A bulk segregant analysis (BSA) approach allowed us to identify and isolate random amplified polymorphic DNA (RAPD) markers linked to the sex chromosomes. From a total of 86 RAPD markers in the parents, 6 markers were found to be linked to the Ys and 1 to the X. Two of the Y-linked markers represent two AT-rich satellite DNAs (satDNAs), named RAYSII and RAYSIII, that share about 80% homology, as well as with RAYSI, another satDNA of R. acetosa. Fluorescent in situ hybridisation demonstrated that RAYSII is specific for Y₁, whilst RAYSIII is located in different clusters along Y₁ and Y₂. The two satDNAs were only detected in the genome of the dioecious species with XX/XY₁Y₂ multiple sex chromosome systems in the subgenus Acetosa, but were absent from other dioecious species with an XX/XY system of the subgenera Acetosa or Acetosella, as well as in gynodioecious or hermaphrodite species of the subgenera Acetosa, Rumex and Platypodium. Phylogenetic analysis with different cloned monomers of RAYSII and RAYSIII from both R. acetosa and R. papillaris indicate that these two satDNAs are completely separated from each other, and from RAYSI, in both species. The three Y-specific satDNAs, however, evolved from an ancestral satDNA with repeating units of 120 bp, through intermediate satDNAs of 360 bp. The data therefore support the idea that Y-chromosome differentiation and heterochromatinisation in the Rumex species having a multiple sex chromosome system have occurred by different amplification events from a common ancestral satDNA. Since dioecious species with multiple XX/XY₁Y₂ sex chromosome systems of the section Acetosa appear to have evolved from dioecious species with an XX/XY system, the amplification of tandemly repetitive elements in the Ys of the section Acetosa is a recent evolutionary process that has contributed to an increase in the size and differentiation of the already non-recombining Y chromosomes.     

Synaptonemal complexes in insects

The synaptonemal complex (SC) is the key nuclear element formed in meiotic prophase I to join 2 homologous chromosomes at the pachytene bivalent. It is a highly conserved structure that is universally present in eukaryotes. The SC is presented as a tripartite protein structure, which consists of 2 lateral elements and a central region. In insects, the central region is particularly distinct and highly ordered. This made it possible to describe the fine structure of the central region and propose a model of its architecture. Chromatid DNA is arranged in chromatin loops extending radially from the SC. The loops appear to consist of a basic chromatin fiber with a diameter of 20–30 nm. In many insect species, synaptonemal polycomplexes occur in postpachytene cells. They represent one of the possible ways of SC degradation. Another process, which occurs beyond pachytene, is the formation of proteinaceous chromatid axis, the silver-stained chromatid core. Based on results in insect models, the chromatid cores have been related to the structure and formation of the SC. Research on insect models significantly contributed to understanding individual steps of the SC formation and temporal sequence of chromosome pairing. These include the formation of lateral elements of the SC, pairing initiation, interlocking of chromosomes, and synapsis of homologous chromosomes. Attention is also given to non-homologous pairing, including synaptic adjustment, correction of pairing, and pairing of sex chromosomes. In the next section, chiasmatic and achiasmatic modes of meiosis are compared with respect to the SC formation. In the chiasmatic mode, the SCs display recombination nodules that are believed to mediate the process of recombination. These nodules were discovered in insects, and indirect evidence for their role comes from insects. Two different examples of achiasmatic meiosis, occurring in the heterogametic sex of several insect orders, are given: one involves the SC formation, whereas in the other, SCs are absent. Finally, the potential of SC karyotyping for analysis of the insect genome is discussed.     

The chicken vimentin gene. Nucleotide sequence, regulatory elements, and comparison to the hamster gene

Here we report the nucleotide sequence of the chicken vimentin gene and its deduced primary amino acid sequence. A comparison of this gene to other intermediate filament protein genes demonstrates that both exon size and position are strongly conserved features of this multigene family. In addition, the hamster and chicken vimentin genes exhibit strong identity at the level of nucleotide (74%) and amino acid (80%) sequence. Interestingly, 40% of total sequence diversity is localized to the N terminus or "head" region of these genes whereas other protein domains (rod and C terminus) are remarkably identical in both nucleotide (81%) and amino acid (89%) sequence. Even stronger amino acid identity (100%) is exhibited in certain subdomains which may define regions crucial for filament formation and function. Not surprisingly, vimentin is more homologous across animal species than it is to other intermediate filament protein members (e.g. desmin) within the same species. A comparison of 5'-flanking sequences of the hamster and chicken genes as well as other characterized promoter elements (SV40, HSV-TK) reveals homologous sequence elements which may define common and/or unique sites involved in the modulation of gene expression. The implications of these sequence elements for both tissue-specific and developmental expression of the vimentin gene are discussed.     

昆虫基因启动子及细胞色素P450基因启动子研究进展

细胞色素P450是一类重要的解毒酶系。昆虫在各种内源或外源性有毒物质的胁迫下,通过调控体内细胞色素P450的过表达,对有毒化合物进行解毒代谢,从而适应不利环境。在昆虫体内,P450基因表达的调控主要发生在转录水平上,启动子作为基因的一部分,能够与RNA聚合酶结合形成转录起始复合体,进而控制基因表达的起始时间和表达程度。基于此,就昆虫启动子的分析及功能验证的主要方法、昆虫启动子的结构特征及昆虫细胞色素P450基因启动予的一些研究进展进行概述,以期为昆虫细胞色素P450基因启动子的深入研究提供借鉴。