Hox genes in the echiuroid Urechis unicinctus

An echiuroid species, Urechis unicinctus, was surveyed for Hox genes using polymerase chain reaction with homeobox-specific degenerate primers. We identified nine distinct homeodomain-containing gene fragments. These nine fragments were classified by comparative analysis. This analysis revealed that this echiuroid possessed at least three Hox genes from the anterior group, five from the central group, and one from the posterior group.     

The duplication of the <Emphasis Type="Italic">Hox</Emphasis> gene clusters in teleost fishes

Higher teleost fishes, including zebrafish and fugu, have duplicated their Hox genes relative to the gene inventory of other gnathostome lineages. The most widely accepted theory contends that the duplicate Hox clusters orginated synchronously during a single genome duplication event in the early history of ray-finned fishes. In this contribution we collect and re-evaluate all publicly available sequence information. In particular, we show that the short Hox gene fragments from published PCR surveys of the killifish Fundulus heteroclitus, the medaka Oryzias latipes and the goldfish Carassius auratus can be used to determine with little ambiguity not only their paralog group but also their membership in a particular cluster. Together with a survey of the genomic sequence data from the pufferfish Tetraodon nigroviridis we show that at least percomorpha, and possibly all eutelosts, share a system of 7 or 8 orthologous Hox gene clusters. There is little doubt about the orthology of the two teleost duplicates of the HoxA and HoxB clusters. A careful analysis of both the coding sequence of Hox genes and of conserved non-coding sequences provides additional support for the “duplication early” hypothesis that the Hox clusters in teleosts are derived from eight ancestral clusters by means of subsequent gene loss; the data remain ambiguous, however, in particular for the HoxC clusters. Assuming the “duplication early” hypothesis we use the new evidence on the Hox gene complements to determine the phylogenetic positions of gene-loss events in the wake of the cluster duplication. Surprisingly, we find that the resolution of redundancy seems to be a slow process that is still ongoing. A few suggestions on which additional sequence data would be most informative for resolving the history of the teleostean Hox genes are discussed. Supplemental material is available at http://www.bioinf.uni-leipzig.de/Publications/SUPPLEMENTS/04-006/.     

<Emphasis Type="Italic">Hox</Emphasis> cluster duplication in the basal teleost <Emphasis Type="Italic">Hiodon alosoides</Emphasis> (Osteoglossomorpha)

Large-scale—even genome-wide—duplications have repeatedly been invoked as an explanation for major radiations. Teleosts, the most species-rich vertebrate clade, underwent a “fish-specific genome duplication” (FSGD) that is shared by most ray-finned fish lineages. We investigate here the Hox complement of the goldeye (Hiodon alosoides), a representative of Osteoglossomorpha, the most basal teleostean clade. An extensive PCR survey reveals that goldeye has at least eight Hox clusters, indicating a duplicated genome compared to basal actinopterygians. The possession of duplicated Hox clusters is uncoupled to species richness. The Hox system of the goldeye is substantially different from that of other teleost lineages, having retained several duplicates of Hox genes for which crown teleosts have lost at least one copy. A detailed analysis of the PCR fragments as well as full length sequences of two HoxA13 paralogs, and HoxA10 and HoxC4 genes places the duplication event close in time to the divergence of Osteoglossomorpha and crown teleosts. The data are consistent with—but do not conclusively prove—that Osteoglossomorpha shares the FSGD. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

The ten Hox genes of the millipede Glomeris marginata

We have isolated the ten Hox genes from the pill millipede Glomeris marginata (Myriapoda:Diplopoda). All ten genes are expressed in characteristic Hox-gene-like expression patterns. The register of Hox gene expression borders is conserved and the expression profiles show that the anterior-most limb-bearing segment in arthropods (antennal/cheliceral segment) does not express any Hox gene, while the next segment (intercalary/second-antennal/premandibular/pedipalpal segment) does express Hox genes. The Hox expression patterns in this millipede thus support the conclusion that all arthropods possess a deuterocerebral segment. We find that there is an apparent posterior shift of Hox gene expression domains dorsally relative to their ventral patterns, indicating that the decoupling of dorsal and ventral segmentation is not restricted to the level of segment polarity genes but apparently includes the Hox genes. Although the mechanism for the decoupling of dorsal and ventral segmentation remains unsolved, the decoupling must be at a level higher in the hierarchy than that of the segment polarity and Hox genes. The expression patterns of Ultrabithorax and abdominal-A suggest a correlation between the function of these genes and the delayed outgrowth of posterior trunk appendages. This delay may be caused by an assumed repressor function of Ultrabithorax, which might partially repress the activation of the Distal-less gene. The Glomeris fushi tarazu gene is expressed in a Hox-like domain and in the developing central nervous system, but not in segmental stripes such as has been reported in another myriapod species, the centipede Lithobius. In contrast to the Lithobius fushi tarazu gene, there is no indication for a role in segment formation for the millipede fushi tarazu gene, suggesting that fushi tarazu first acquired its segmentation function in the lineage of the insects.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

In Bradyrhizobium japonicum the common nodulation genes, nodABC, are linked to nifA and fixA

Summary Using cloned Rhizobium phaseoli nodulation (nod) genes as hybridization probes homologous restriction fragments were detected in the genome of the slow-growing soybean symbiont, Bradyrhizobium japonicum strain 110. These fragments were isolated from a cosmid library, and were shown to lie 10 kilobasepairs (kb) upstream from the nifA and fixA genes. Specific nod probes from Rhizobium leguminosarum were used to identify nodA-, nodB-, and nodC-like sequences clustered within a 4.5 kb PstI fragment. A mutant was constructed in which the kanamycin resistance gene from Tn5 was inserted into the nodA homologous B. japonicum region. This insertion was precisely located, by DNA sequencing, to near the middle of the nodA gene. B. japonicum mutants carrying this insertion were completely nodulation deficient (Nod^-).     

Seven Hox gene sequences from the asterinid starfish Patiriella exigua (Echinodermata: Asteroidea)

Partial homeobox gene fragments were amplified from Patiriella exigua genomic DNA by PCR using degenerate primers. The primers spanned a region of 82 nucleotides within the homeobox, encompassing amino acids 21–47 of the homeodomain. The deduced amino acid sequences of the seven Hox gene sequences plus one Xlox-type gene sequence from P. exigua are presented and compared with similar sequences from other organisms. This work is a preliminary step in the analysis of the evolution of development in the Patiriella species group and the roles of Hox gene expression therein.     

Mutations in somePolycomb group genes ofDrosophila interfere with regulation of segmentation genes

Mutations in severalPolycomb (Pc) group genes cause maternal-effect or zygotic segmentation defects, suggesting thatPc group genes may regulate the segmentation genes ofDrosophila. We show that individuals doubly heterozygous for mutations inpolyhomeotic and six otherPc group genes show gap, pair rule, and segment polarity segmentation defects. We examined double heterozygous combinations ofPc group and segmentation mutations for enhancement of adult and embryonic segmentation defects.Posterior sex combs andpolyhomeotic interact withKrüppel ² and enhance embryonic phenotypes ofhunchback andknirps, andpolyhomeotic enhanceseven-skipped. Surprisingly, flies carrying duplications ofextra sex combs (esc), that were heterozygous for mutations ofeven-skipped (eve), were extremely subvital. Embryos and surviving adults of this genotype showed strong segmentation defects in even-numbered segments. Antibody studies confirm that expression ofeve is suppressed by duplications ofesc. However,esc duplications have no effect on other gap or pair rule genes tested. To our knowledge, this is only the second triplo-abnormal phenotype associated withPc group genes. Duplications of nine otherPc group genes have no detectable effect oneve. Expression ofengrailed (en) was abnormal in the central nervous systems of mostPc group mutants. These results support a role forPc genes in regulation of some segmentation genes, and suggest thatesc may act differently from otherPc group genes.     

大豆GeBP转录因子基因家族的生物信息学分析

GeBP转录因子调控植物表皮毛的生长发育,并且参与控制植物叶片的发育。该文利用生物信息学方法,在大豆全基因组范围内搜索GeBP基因家族,并从氨基酸理化性质、基因结构、染色体的物理分布、系统进化、序列比对、功能结构域、组织表达情况等基本特征方面对GmGeBP基因家族进行分析。结果表明:(1)共获得9个GmGeBP转录因子基因家族成员,其中仅2个基因含有内含子,且都只有1个内含子,表明该家族成员基因构造比较简单但稳定。(2)GmGeBP编码的蛋白分子量为39.65~49.24 kD,理论等电点为4.65~9.08;这些成员基本上都是酸性氨基酸,属于亲水性、不稳定蛋白。(3)这9个基因不均匀的分布于7条染色体上,10和20号染色体上分别分布2个GeBP基因,3、5、13、15、19号染色体上各分布1个基因。(4)系统进化分析表明,大豆与拟南芥对应的GeBP成员亲缘关系较近,分别聚类到4个分支,而与水稻的距离较远。(5)结构域分析表明,9个GmGeBP成员都包含DUF573结构域,推测该部分在GeBP转录因子中很可能是与靶标基因顺式作用元件互作的结构域。(6)通过分析大豆GmGeBP转录因子基因家族的组织表达,发现不同基因在大豆不同组织的表达量不同,具有一定的特异性。该文对大豆GeBP转录因子基因家族的分析和鉴定为进一步研究大豆表皮毛发育的分子作用提供了理论基础。     

赤桉ACT1和ACT2基因的克隆与生物信息学分析

为了解赤桉(Eucalyptus camaldulensis)肌动蛋白(Actin)在生长发育过程中的功能,根据赤桉幼苗转录组数据库中的肌动蛋白基因序列,从赤桉嫩叶中克隆了2条Actin基因片段,并利用RACE技术获得Actin基因的全长cDNA,分别命名为ECACT1和EC-ACT2基因。生物信息学分析表明,这两条基因的全长cDNA分别为1533 bp和1387 bp,均含有1个编码377个氨基酸的开放阅读框。经比对分析,赤桉Actin蛋白的氨基酸序列与其他植物Actin蛋白的具有较高的相似性,并且具有Actin蛋白特有的保守序列和相关特征。因此推测这两条基因对桉树的生长发育具有一定的调控作用。     

Isolation and expression analysis of a poriferan <Emphasis Type="Italic">Antp</Emphasis>-class <Emphasis Type="Italic">Bar-/Bsh-</Emphasis>like homeobox gene

A novel non-Hox Antp-class gene (BarBsh-Hb) was isolated from the marine sponge Halichondria sp. This gene shares high sequence identity with eumetazoan genes from the Bsh and Bar gene families and can be distinguished from other non-Hox Antp-class genes by diagnostic residues. We also present an alignment of all known (full-length) poriferan non-Hox Antp-class genes. Maximum likelihood methods were employed to estimate phylogenetic relationships among non-Hox genes and BarBsh-Hb. We employed RT-PCR techniques to look at expression across different developmental stages (larval to rhagon). BarBsh-Hb product was present in newly released larvae, but expression was not detected 8–16 h post-release. Expression of BarBsh-Hb was detected in later-stage (>16 h post-release), free-swimming larvae until they settled and attached to the substratum, after which expression was down-regulated. In a separate set of experiments, low levels of expression were observed in normal adult tissue and disaggregated adult tissue, but BarBsh-Hb expression increased during tissue re-aggregation. These data increase the number of non-Hox homeobox genes identified in sponges and provide evidence of regulation of this non-Hox gene during sponge development. While the Bar and Bsh genes play important roles in the development of nervous tissue—especially visual systems—in metazoans, the specific role(s) BarBsh-Hb play(s) in sponge development is unclear and deserves greater attention.Edited by C. Desplan     

同源盒基因(Hox)与哺乳动物生殖

哺乳动物的同源盒基因（Hox）与果蝇的同源异形基因是同源基因,该基因编码的DNA片段含183碱基对,转录由61个氨基酸残基组成的蛋白质保守结构域,称同源异型域.Hox基因碱基顺序及在染色体中的位置都是高度保守的.Hox基因在体节结构分化等空间信息调控中起着重要作用,按特异的空间模式赋予每一体节其自身的特点.近年来的研究表明,Hox基因不但影响胚胎发育,而且与成体生殖系统分化有关,在着床期子宫接受态的建立及子宫蜕膜反应的发生等生殖过程中起着重要的调节作用.     

Characterization of recA genes and recA mutants of Rhizobium meliloti and Rhizobium leguminosarum biovar viciae

Summary DNA fragments carrying the recA genes of Rhizobium meliloti and Rhizobium leguminosarum biovar viciae were isolated by complementing a UV-sensitive recA ^– Escherichia coli strain. Sequence analysis revealed that the coding region of the R. meliloti recA gene consists of 1044 by coding for 348 amino acids whereas the coding region of the R. leguminosarum bv. viciae recA gene has 1053 bp specifying 351 amino acids. The R. meliloti and R. leguminosarum bv. viciae recA genes show 84.8% homology at the DNA sequence level and of 90.1% at the amino acid sequence level. recA ^– mutant strains of both Rhizobium species were constructed by inserting a gentamicin resistance cassette into the respective recA gene. The resulting recA mutants exhibited an increased sensitivity to UV irradiation, were impaired in their ability to perform homologous recombination and showed a slightly reduced growth rate when compared with the respective wild-type strains. The Rhizobium recA strains did not have altered symbiotic nitrogen fixation capacity. Therefore, they represent ideal candidates for release experiments with impaired strains.The accession numbers: X59956 R. LEGUMINOSARUM REC A ALAS-DNA; X59957 R. MELITOTI REC A ALAS-DNA     

Coordinated spatial and temporal expression ofHox genes during embryogenesis in the acoelConvolutriloba longifissura

Background  

Hox genes are critical for patterning the bilaterian anterior-posterior axis. The evolution of their clustered genomic arrangement and ancestral function has been debated since their discovery. As acoels appear to represent the sister group to the remaining Bilateria (Nephrozoa), investigatingHox gene expression will provide an insight into the ancestral features of theHox genes in metazoan evolution.     

The analysis of core and symbiotic genes of rhizobia nodulating Vicia from different continents reveals their common phylogenetic origin and suggests the distribution of Rhizobium leguminosarum strains together with Vicia seeds

In this work, we analysed the core and symbiotic genes of rhizobial strains isolated from Vicia sativa in three soils from the Northwest of Spain, and compared them with other Vicia endosymbionts isolated in other geographical locations. The analysis of rrs, recA and atpD genes and 16S–23S rRNA intergenic spacer showed that the Spanish strains nodulating V. sativa are phylogenetically close to those isolated from V. sativa and V. faba in different European, American and Asian countries forming a group related to Rhizobium leguminosarum. The analysis of the nodC gene of strains nodulating V. sativa and V. faba in different continents showed they belong to a phylogenetically compact group indicating that these legumes are restrictive hosts. The results of the nodC gene analysis allow the delineation of the biovar viciae showing a common phylogenetic origin of V. sativa and V. faba endosymbionts in several continents. Since these two legume species are indigenous from Europe, our results suggest a world distribution of strains from R. leguminosarum together with the V. sativa and V. faba seeds and a close coevolution among chromosome, symbiotic genes and legume host in this Rhizobium–Vicia symbiosis.     

The FUSCA genes of Arabidopsis: negative regulators of light responses

More than 200 fusca mutants of Arabidopsis have been isolated and characterised, defining 14 complementation groups. Mutations in at least nine FUSCA genes cause light-dependent phenotypic changes in the absence of light: high levels of anthocyanin accumulation in both the embryo and the seedling, inhibition of hypocotyl elongation, apical hook opening, and unfolding of cotyledons. In double mutants, the fusca phenotype is epistatic to the hy phytochromedeficiency phenotype, indicating that the FUSCA genes act downstream of phytochrome. By contrast, the accumulation of anthocyanin is suppressed by mutations in TT and TTG genes, which affect the biosynthesis of anthocyanin, placing the FUSCA genes upstream of those genes. Regardless of the presence or absence of anthocyanin, fusca mutations limit cell expansion and cause seedling lethality. In somatic sectors, mutant fus1 cells are viable; expressing tissue-specific phenotypes: reduced cell expansion and accumulation of anthocyanin in subepidermal tissue, formation of ectopic trichomes but no reduced cell expansion in epidermal tissue. Our results suggest a model of FUSCA gene action in light-induced signal transduction.     

Genome Analysis inNeurospora crassa;Cloning of Four Lociarginine-1(arg-1),methionine-6(met-6),unknown-7(un-7), andribosome production-1(rip-1) and Associated Chromosome Walking

We have cloned fourNeurospora crassagenes by complementation analysis. Cloned genes include thearginine-1(arg-1),methionine-6(met-6),unknown-7(un-7), andribosome production-1(rip-1) loci. Chromosome walks were initiated in ordered cosmid libraries from the cloned loci. A total of about 700 kb of theNeurosporagenome is covered in these walks.