The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease

Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.     

Comparative analysis of protein kinases and associated domains between Ascomycota and Basidiomycota

Protein kinases play an important role in every aspect of cellular life. In this study, we systemically identified protein kinases from the predicted proteomes of 59 representative fungi from Ascomycota and Basidiomycota. Comparative analysis revealed that fungi from Ascomycota and Basidiomycota differed in the number and variety of protein kinases. Some groups of protein kinases, such as calmodulin/calcium regulated kinases (CMGC) and those with the highest group percentages are the most prevalent protein kinases among all fungal species tested. In contrast, the STE group (homologs of the yeast STE7, STE11 and STE20 genes), was more abundant in Basidiomycetes than in Ascomycetes. Importantly, the distribution of some protein kinase families appeared to be subphylum-specific. The tyrosine kinase-like (TKL) group had a higher protein kinase density in Agaricomycotina fungi. In addition, the distribution of accessory domains, which could have functional implications, demonstrated that usage bias varied between the two phyla. Principal component analysis revealed a divergence between the main functional domains and associated domains in fungi. This study provides novel insights into the variety and expansion of fungal protein kinases between Ascomycota and Basidiomycota.     

小麦PR5Ks蛋白家族鉴定与分析

类PR5受体蛋白激酶（PR5 receptor-like protein kinase,PR5Ks）包含病程相关蛋白5(PR5)和激酶结构域,为植物类受体蛋白激酶（Receptor-like protein kinase,RLK）家族的1个亚族,与植物的抗病防御反应相关。本研究从小麦基因组中鉴定了17个PR5Ks基因,对其理化性质、基因结构、保守基序和启动子进行分析。结果表明,17个PR5Ks蛋白家族成员均为疏水性蛋白,氨基酸数目在415～663个,分子量在44.60～73.52 kD,等电点介于5.61～8.4,蛋白结构以无规则卷曲和α螺旋为主。顺式作用元件分析显示,在小麦PR5Ks基因转录起始位点上游2 000 bp序列中存在多种响应元件,包括SA、MeJA、厌氧诱导、低温等响应元件。为了明确17个小麦PR5Ks成员是否具有抗病性,对小麦在赤霉菌（Fusarium graminearum）和条锈菌（Puccinia striiformisf. sp.tritici）侵染过程中PR5Ks基因的表达规律进行分析,发现TaPR5K-3、TaPR5K-5、TaPR5K-9和TaPR5K-11受赤霉菌和条锈菌的共同诱导。利用实时荧光定量PCR(Quantitative real-time PCR,qPCR)技术检测了接种叶锈菌的小麦中基因的表达模式,结果显示,TaPR5K-3、TaPR5K-5、TaPR5K-9和TaPR5K-11这4个基因均受叶锈菌诱导且在抗病植株中高表达,表明他们在小麦与叶锈菌的互作中发挥正向调控作用。综上所述,本研究初步筛选到4个与小麦抗病相关的PR5Ks基因,为进一步揭示PR5Ks蛋白家族参与小麦生长发育及抗病防御反应提供参考。     

Activated signal transduction kinases frequently occupy target genes

Cellular signal transduction pathways modify gene expression programs in response to changes in the environment, but the mechanisms by which these pathways regulate populations of genes under their control are not entirely understood. We present evidence that most mitogen-activated protein kinases and protein kinase A subunits become physically associated with the genes that they regulate in the yeast (Saccharomyces cerevisiae) genome. The ability to detect this interaction of signaling kinases with target genes can be used to more precisely and comprehensively map the regulatory circuitry that eukaryotic cells use to respond to their environment.     

Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees

The determination of the chimpanzee genome sequence provides a means to study both structural and functional aspects of the evolution of the human genome. Here we compare humans and chimpanzees with respect to differences in expression levels and protein-coding sequences for genes active in brain, heart, liver, kidney, and testis. We find that the patterns of differences in gene expression and gene sequences are markedly similar. In particular, there is a gradation of selective constraints among the tissues so that the brain shows the least differences between the species whereas liver shows the most. Furthermore, expression levels as well as amino acid sequences of genes active in more tissues have diverged less between the species than have genes active in fewer tissues. In general, these patterns are consistent with a model of neutral evolution with negative selection. However, for X-chromosomal genes expressed in testis, patterns suggestive of positive selection on sequence changes as well as expression changes are seen. Furthermore, although genes expressed in the brain have changed less than have genes expressed in other tissues, in agreement with previous work we find that genes active in brain have accumulated more changes on the human than on the chimpanzee lineage.     

鸡下丘脑组织表达序列标签的测定与分析

在构建cDNA文库的基础上，测定了83个鸡下丘脑组织表达序列标签。结果表明：50个KST可以在Genbanl（中找到同源序列，其中12个为线粒体基因，12个为功能未知EST，21个为新EST。对50个具有同源序列的EST进行了功能分类。已知EST和未知EST的蛋白阅读框预测及与蛋白质数据库同源性比较结果表明：克隆CHH0014、CHH0022、CHH0028、CHHD21均获得了同源性较高的同源产物，其中克隆CHH0022、CHH0028和CHHD21均有多个物种的不同蛋白与之同源。     

The protein kinase family: conserved features and deduced phylogeny of the catalytic domains

In recent years, members of the protein kinase family have been discovered at an accelerated pace. Most were first described, not through the traditional biochemical approach of protein purification and enzyme assay, but as putative protein kinase amino acid sequences deduced from the nucleotide sequences of molecularly cloned genes or complementary DNAs. Phylogenetic mapping of the conserved protein kinase catalytic domains can serve as a useful first step in the functional characterization of these newly identified family members.     

Metagenomic analysis of the human distal gut microbiome

The human intestinal microbiota is composed of 10(13) to 10(14) microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed approximately 78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction-amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway-mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.     

Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs)

Analysis of the human and mouse genomes identified an abundance of conserved non-genic sequences (CNGs). The significance and evolutionary depth of their conservation remain unanswered. We have quantified levels and patterns of conservation of 191 CNGs of human chromosome 21 in 14 mammalian species. We found that CNGs are significantly more conserved than protein-coding genes and noncoding RNAS (ncRNAs) within the mammalian class from primates to monotremes to marsupials. The pattern of substitutions in CNGs differed from that seen in protein-coding and ncRNA genes and resembled that of protein-binding regions. About 0.3% to 1% of the human genome corresponds to a previously unknown class of extremely constrained CNGs shared among mammals.     

Multiple, distinct forms of bovine and human protein kinase C suggest diversity in cellular signaling pathways

A new family of protein kinase C-related genes has been identified in bovine, human, and rat genomes. The alpha-, beta-, and gamma-type protein kinase sequences are highly homologous, include a kinase domain, and potential calcium-binding sites, and they contain interspersed variable regions. The corresponding genes are located on distinct human chromosomes; the possibility of even greater genetic complexity of this gene family is suggested by Northern and Southern hybridization analyses.     

Identification and Bioinformatics Analysis of SnRK2 and CIPK Family Genes in Sorghum

Through bioinformatic data mining, 10 SnRK2 and 31 CIPK genes were identified from sorghum genome. They are unevenly distributed in the sorghum chromosomes. Most SnRK2 genes have 8 introns, while the CIPK genes have a few （no intron or less than 3 introns） or more than I0 introns. Phylogenetic analysis revealed that SnRK2 genes belong to one cluster and CIPK genes form the other independent cluster. The sorghum SnRK2s are subgrouped into three parts, and CIPK into five parts. More than half SnRK2 and CIPK genes present in homologous pairs, suggesting gene duplication may be due to the amplification of SnRK family genes. The kinase domains of SnRK2 family are highly conserved with 88.40% identity, but those of the CIPK family are less conserved with 63.72% identity. And the identity of sorghum CBLinteracting NAF domains of CIPKs is 61.66%. What＇s more, regarding to the sorghum SnRK2 and CIPK kinases, they are characterized with distinct motifs and their subcellular localization is not necessarily the same, which suggests they may be divergent in functions. Due to less conserved sequences, complex subcellular localization, and more family members, sorghum CIPK genes may play more flexible and multiple biological functions. According to the phylogenetic analysis of SnRK genes and SnRK functional studies in other plants, it is speculated that sorghum SnRK2 and CIPK genes may play important roles in stress response, growth and development.     

Genome of the host-cell transforming parasite Theileria annulata compared with T. parva

Theileria annulata and T. parva are closely related protozoan parasites that cause lymphoproliferative diseases of cattle. We sequenced the genome of T. annulata and compared it with that of T. parva to understand the mechanisms underlying transformation and tropism. Despite high conservation of gene sequences and synteny, the analysis reveals unequally expanded gene families and species-specific genes. We also identify divergent families of putative secreted polypeptides that may reduce immune recognition, candidate regulators of host-cell transformation, and a Theileria-specific protein domain [frequently associated in Theileria (FAINT)] present in a large number of secreted proteins.     

野生大豆CDPK基因保守区的克隆及序列分析

CDPK(Ca2+-dependent,calmodulinindependentproteinkinase)是植物钙信号传导过程中关键的蛋白激酶,在逆境胁迫信号传导过程中起到重要作用。研究基于同源序列候选基因的策略,根据已经公布的多个CDPK序列的比对结果,在保守性较高的区域,设计两对巢式简并引物,结合降落PCR和巢式PCR在野生大豆中克隆。对获得的序列片段进行序列分析,发现该序列具有激酶活性的功能区域和CDPK特有的EF手性结构区,并且与VrCDPK(U08140)序列达到94%的相似性,可以确定该片段是CDPK基因的保守序列。结果证明,野生大豆中也存在CDPK基因,并为通过RACE等方法获得野生大豆全长CDPK基因奠定了基础。     

The genome of the sea urchin Strongylocentrotus purpuratus

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.     

Evolution of key cell signaling and adhesion protein families predates animal origins

The evolution of animals from a unicellular ancestor involved many innovations. Choanoflagellates, unicellular and colonial protozoa closely related to Metazoa, provide a potential window into early animal evolution. We have found that choanoflagellates express representatives of a surprising number of cell signaling and adhesion protein families that have not previously been isolated from nonmetazoans, including cadherins, C-type lectins, several tyrosine kinases, and tyrosine kinase signaling pathway components. Choanoflagellates have a complex and dynamic tyrosine phosphoprotein profile, and cell proliferation is selectively affected by tyrosine kinase inhibitors. The expression in choanoflagellates of proteins involved in cell interactions in Metazoa demonstrates that these proteins evolved before the origin of animals and were later co-opted for development.     

基因组水平上水稻受体激酶基因家族的生物信息学分析

 对已完成全序列分析的籼稻(北京基因组信息中心,BGI)和接近完成全序列分析的粳稻(国际水稻基因组测序计划,IRGSP)的蛋白质数据库进行两步HMM(hidden markov model)模式匹配搜寻,在基因组水平上分别获得籼稻和粳稻受体激酶5个基因家族的成员序列共643和701个,对粳稻受体激酶进行了详细的生物信息学分析。对粳稻和籼稻的同源比较分析表明,受体激酶基因存在非常强的保守性,但不同基因在基因组水平上可能存在不同水平的扩增。对Swissprot数据库的同源分析表明,这些基因是植物特有的受体激酶。搜     

木薯25个WRKY家族转录因子在生物胁迫下的表达分析

根据拟南芥和水稻的WRKY基因和木薯基因组序列,利用生物信息学方法预测木薯Me WRKY转录因子家族成员,并对其进行系统进化关系和保守结构域的分析。通过病原菌接种处理,分析不同Me WRKY转录因子的表达差异。结果显示,木薯共编码25个与抗病相关WRKY蛋白,在病原菌胁迫条件下,其中16个Me WRKY基因的表达受到显著影响,表明这些WRKY蛋白可能参与木薯的防御应答反应。