Sequence Analysis of a 685-kb Genomic Region on Chromosome 3p22-p21.3 That Is Homozygously Deleted in a Lung Carcinoma Cell Line

Frequent chromosomal aberrations and/or losses of heterozygosityinvolving the short arm of chromosome 3 in carcinomas of thelung, kidney and other tissues imply that multiple putativetumor suppressor genes may be present on this chromosomal arm.To search for one of these genes, we determined DNA sequencesin the genomic region at 3p22–21.3 where we had previouslydetected a homozygous deletion in a lung cancer cell line. TheDNA sequence results of an about 685-kb region indicated thatthe size of the homozygously deleted segment was 638,489 bp,in which we identified only four genes including the integrinRLC and the trans-Golgi p230 genes, both reported previously.The predicted amino acid sequences of one of the two novel genesshowed high homology to villin, a human cytoskeleton protein;those of the other gene, termed HYA22, revealed significanthomology to YA22, a hypothetical protein predicted from DNAsequences of Schizosaccharomyces pombe. The computer programsHEXON or GRAIL were able to predict three-fourths of the exons;the smallest exon predicted by either program was 46 base pairs.Repetitive sequences contained in the genomic region included151 copies of the Alu sequence (1 copy/every 4.5 kb), 19 copiesof the L1 sequence (1 copy/every 36 kb) , and 10 copies of theTHE sequence.     

小菜蛾烟碱型乙酰胆碱受体α亚基cDNA的克隆、序列分析与不同发育阶段表达分析

烟碱型乙酰胆碱受体(nAChR)介导昆虫中枢神经系统中胆碱能突触兴奋性神经递质的快速传递,也是新烟碱类杀虫剂和多杀菌素的作用靶标。本研究利用RT-PCR和RACE技术,克隆了小菜蛾Plutella xylostella nAChR α亚基的一个新基因(Pxα8)的全长cDNA(GenBank登录号为EU914853)。Pxα8的cDNA序列全长1 744 bp,开放阅读框为1 602 bp,编码534个氨基酸,具有nAChR α亚基的典型特征,与其他昆虫nAChR α8亚基具有77%～96%的相似性,与果蝇nAChR β2亚基具有76%的相似性。Pxα8的开放阅读框存在单核苷酸多态性位点,导致多个位点氨基酸的替换。雌性4龄幼虫的多态性位点多于雄性4龄幼虫,而且雌、雄4龄幼虫的多态性位点均不相同。半定量RT-PCR研究结果表明,Pxα8 mRNA在成虫期表达量高于蛹期和4龄幼虫期。本研究结果为进一步研究小菜蛾nAChR 亚基的多样性和对多杀菌素的靶标抗性机制提供重要基础。     

Conserved amino acid residues within and outside of the N-terminal ribonucleoprotein motif of U1A small nuclear ribonucleoprotein involved in U1 RNA binding

By the use of hybrids between a U1 small nuclear ribonucleoprotein (snRNP: U1A) and a U2 snRNP (U2B") we have identified regions containing 29 U1A-specific amino acid residues scattered throughout the 117 N-terminal residues of the protein, which are involved in binding to U1 RNA. The U1A-specific amino acid residues have been arbitrarily divided into seven contiguous groups. None of these groups is sufficient for U1 binding when transferred singly into the U2B" context, and none of the groups is essential for U1 binding in U1A. Several different combinations of two or more groups can, however, confer the ability to bind U1 RNA to U2B", suggesting that most or all of the U1A-specific amino acid residues contribute incrementally to the strength of the specific binding interaction. Further evidence for the importance of the U1A-specific amino acid residues, some of which lie outside the region previously shown to be sufficient for U1 RNA binding, is obtained by comparison of the sequence of human and Xenopus laevis U1A cDNAs. These are extremely similar (94.4% identical) between amino acid residues 7 and 114 but much less conserved immediately upstream and downstream from this region.     

一个鼻咽癌相关EST的鉴定及其全长cDNA序列分析

鼻咽癌是我国南方及东南亚地区常见的恶性肿瘤之一.通过对鼻咽癌染色体高频率杂合性丢失区域3p21的表达序列标签(expressedsequencetag,EST)进行同源性比较分析,运用逆转录聚合酶链式反应的方法,筛选到一个在41.18%(14/34)的鼻咽癌活检组织及20.0%(1/5)的鼻咽癌细胞系中表达下调的ESTBG772301;并用Northern杂交方法,检测了该EST在多种正常成人组织中的表达状况及其所代表基因的转录本大小.在此基础上,对该EST来源的cDNA克隆(IMAGE:4839190)进行直接测序,获得了一个全长为2377bp的新cDNA序列;经生物信息学分析,发现它与已知基因序列无明显同源性,属于一个新基因,定位于染色体3p21.3,被命名为鼻咽癌表达下调基因(NPCEDRG,GenBank登录号:AF538150).其编码的蛋白质含169个氨基酸,与一个已报道的在进化上相对保守、功能未知的人类蛋白Nicolin1(简称NICN1)N端170个氨基酸残基的序列同源性为97%,但缺少NICN1蛋白C端43个氨基酸残基,可能是nicolin1基因不同剪接本的编码产物.     

烟夜蛾组织蛋白酶B酶原基因的克隆、序列分析和原核表达

利用反转录多聚酶链式反应（RT-PCR）技术从烟夜蛾Helicoverpa assulta (Guenée)雌虫卵巢中扩增得到了组织蛋白酶B酶原基因（cathepsin B,CB）cDNA片段,将其克隆至pMD19-T载体。测序结果表明, 该片段长度为1 017 bp,含有组织蛋白酶B酶原基因完整开放阅读框架（ORF）（GenBank登录号：EF154237）。序列分析结果显示：烟夜蛾组织蛋白酶B（HassCB）编码338个氨基酸残基,预测N-末端含有长度为21个氨基酸残基的信号肽序列;去除信号肽序列后,预测成熟蛋白分子量为35.5 kDa,等电点为5.96。氨基酸序列比对结果表明,HassCB与其他昆虫的组织蛋白酶B酶原氨基酸序列有较高的一致性。将去除信号肽序列的HassCB（HassCBa）重组到表达载体pGEX-4T-1中,并转入原核细胞中表达,SDS-PAGE和Western印迹分析表明：该基因能在大肠杆菌BL21中表达,电泳检测到一条大约61 kDa的目的条带,与预测的融合蛋白分子量相符。用该基因制备多克隆抗体并测得该抗体对重组表达的HassCBa的效价为1∶51 200。通过免疫印迹检测证实,此抗体既能识别重组表达的HassCBa,又能识别烟夜蛾卵巢匀浆液中的HassCB。     

Changes in the Levels of Free Amino Acids in Various Regions of Cuscuta during Growth

The angiospermous plant parasite Cuscuta derives reduced carbonand nitrogen compounds primarily from its host. Free amino acidsalong Cuscuta vines in three zones, viz., 0 to 5 cm, 5 to 15cm, and 15 to 30 cm, which in a broad sense represent the regionof cell division, cell elongation and differentiation and vasculartissue differentiation respectively, were quantitatively estimated.The free amino acid content was the highest in the 0 to 5 cmregion and progressively decreased along the posterior regionsof the vine. The haustorial region showed the lowest contentof free amino acids. In general, the free amino acid contentin samples collected at 7 p.m. was found to be higher than thatin the samples collected at 7 a.m. Three basic amino acids,histidine, the uncommon amino acid -hydroxyarginine, and arginineconstituted more than 50% of the total free amino acids in allthe zones studied except the haustorial region. Aspartic acidand glutamic acid constituted the major portion in the acidicand neutral fraction of amino acids. Glutamine, asparagine,threonine, and serine were eluted together and occurred in substantialamounts. -Hydroxyarginine constituted the largest fraction inthe cut end exudate of Cuscuta and presumably appeared to bethe major form of transport amino acid. -Hydroxyarginine wasalso a major constituent of the basic amino acids in Cuscutavines parasitizing host plants from widely separated families,suggesting that this amino acid is a biosynthetic product ofthe parasite rather than that of the hosts. Also, U-¹⁴C argininewas converted to -hydroxyarginine by cut Cuscuta vines, suggestingthat -hydroxyarginine is synthesized de novo from arginine byCuscuta. (Received March 30, 1987; Accepted June 7, 1988)     

Nucleotide sequence of a cloned cDNA copy of TMV (cowpea strain) RNA, including the assembly origin, the coat protein cistron, and the 3'' non-coding region

Summary The cloned cDNA derived from the 3 end of cowpea strain (Cc) RNA of tobacco mosaic virus (TMV) has been sequenced. Substantial sequence information of 1,060 nucleotides from the 3 end of the RNA reveals some interesting features: (1) the coat protein cistron corresponds to residues 210–701 from the 3 end. Some errors in the amino acid sequence previously reported have been corrected and the revised total length of the coat protein is 162 amino acid residues. The capping site of the coat protein mRNA is at residue 711 from the 3 end of genome RNA. (2) The assembly origin of reconstitution is positioned within the coat protein cistron at residue 369–461 which can be formed into a highly base-paired hairpin loop structure. The sequence, GAXGUUG, in the loop region and a triplet-repeated purine base tract surrounding the loop are found. These structural features are common to assembly origins of both Cc and vulgare strains. (3) We find the sequence highly homologous to, but distinct from, the genuine assembly origin. It will be called the pseudo-assembly origin, which is located in the corresponding region to the assembly origin of the vulgare strain, outside the coat protein cistron. There is also the sequence, GAXGUUG, in the middle of the region. (4) In the 5 flanking region of the coat protein cistron, a long reading frame, probably of 30 K protein, is found. The coding region is terminated in the coat protein cistron and thus the 30 K protein and the coat protein cistrons overlap. (5) The 3 non-coding region is 209 residues long and can be folded into a possible tRNA-like structure. Surprisingly, we find that the 3 terminal sequence of Cc RNA is not very similar to that of vulgare RNA but extensively homologous to that of turnip yellow mosaic virus (TYMV) RNA.     

Identification and analysis of novel amino acid sequence repeats and domains in Pyrobaculum aerophilum using computational tools

We have identified four repeats and five domains that are novel in proteins encoded by the Pyrobaculum aerophilum str. IM2 proteome using automated in silico methods. A "repeat" corresponds to a region comprising less than 55 amino acid residues that occurs more than once in the protein sequence and sometimes present in tandem. A "domain" corresponds to a conserved region comprising greater than 55 amino acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1) 85 amino acid residues AAG domain, (2) 72 amino acid residues GFGN domain, (3) 43 amino acid residues KGG repeat, (4) 25 amino acid residues RWE repeat, (5) 25 amino acid residues RID repeat, (6) 108 amino acid residues NDFA domain, (7) 140 amino acid residues VxY domain, (8) 35 amino acid residues LLPN repeat and (9) 98 amino acid residues GxY domain. A repeat or domain is characterized by specific conserved sequence motifs. We discuss the presence of these repeats and domains in proteins from other genomes and their probable secondary structure.     

Cloning of a novel scavenger receptor cysteine-rich type I transmembrane molecule (M160) expressed by human macrophages

We report the cloning of a novel human type I cell surface Ag mainly expressed by macrophages. The primary structure was established by molecular cloning, which yielded a 4579-bp cDNA sequence encoding a polypeptide chain of 1453 amino acid residues with 16 potential N:-glycosylation sites. We designated this molecule M160. The domain organization features 12 scavenger receptor cysteine-rich domains followed by a transmembrane region and a cytoplasmic domain that occurs in two forms, a predominant form (M160-alpha) of 71 residues and an alternatively spliced form (M160-ss) of 39 residues. M160-alpha contains three possible phosphorylation sites, which are lost in the alternatively spliced form. RT-PCR analyses showed M160 to be expressed by alveolar macrophages and by the monocyte cell lines HL60, U937, and THP1, but not by Jurkat or Raji cells. Stimulation of U937 cells with phorbol ester resulted in an increased expression of M160 from day 5 onward. RT-PCR analysis of 19 different human tissues showed signals for M160-alpha of varying intensity in all tissues, whereas M160-ss was confined to the spleen. We conclude that M160 is a new member of the scavenger receptor cysteine-rich superfamily expressed by the monocyte/macrophage cell lineage.     

Conserved and nonconserved structures in the secretory proteins encoded in the Balbiani ring genes ofChironomus tentans

Summary The large, repetitive Balbiani ring (BR) genes, BR 1, 2, and 6, inChironomus tentans originated from a short ancestral sequence and have all evolved according to analogous amplification schemes. We analyzed the structures of the BR-encoded secretory proteins and defined the parts that have been conserved during the evolutionary process. The BR products show striking similarities, with the BR 1 and BR 2 products being more similar to each other than to the BR 6 product. In the constant (C) region of the repeat units, 7 of the 30 amino acid residues are strictly conserved; 4 of these are the cysteine residues. The subrepeat (SR) regions of all the BR products are dominated by repeated tripeptide elements rich in proline and charged amino acid residues. Most of the amino acid replacements in both regions are conservative. Secondary structure predictions suggested that the C regions of the BR 1 and BR2 products have several elements of secondary structure: an -helix, a -strand, and one or two reverse turns, as in globular structures. The prediction for the C region of the BR 6 product is similar but lacks a -strand. The predictions for the intervening SR regions appear less conclusive, but are clearly different from those for the C regions, and suggest regular structures not differing in their conformational elements. The SR regions evolved from an ancestor sequence similar to the C region; thus, the BR products seem to represent an example of evolution from one structure to two differently folded products. It is proposed that the alignment and polymerization of the long BR proteins could be promoted by the repetitive structure of the molecules, due to the possibility of forming disulfide bridges between half-cystine residues and electrostatic interactions between the charged residues of the SR regions. The divergence among the BR products is discussed in relation to possible functional differences among the members of the BR gene family.     

拟黑多刺蚁雌激素相关受体基因cDNA的克隆及生物信息学分析

雌激素相关受体（estrogen related receptors, ERRs）能够直接与类固醇激素受体共激活子（steroidhormone receptor coactivator,SRC）结合,激活靶基因的表达,与众多生理和发育过程有关.采用RT-PCR、RACE等方法从拟黑多刺蚁Polyrhachis vicina Roger克隆得到了雌激素相关受体基因的cDNA克隆,命名为pvERR （GenBank 登录号为EF474463）,并采用生物信息学方法对其cDNA和编码的蛋白质的理化性质、蛋白质二级及三级结构、分子系统进化关系等进行了预测和推断.结果表明：pvERR基因cDNA全长1 935 bp,包含一个1 305 bp的开放阅读框、245 bp的5′-UTR 和385 bp的3′-UTR,编码一个由434个氨基酸组成的蛋白质.pvERR的配体结合区（ligand binding domain,LBD）主要由两个β折叠和11个α螺旋（H1, H3～H12, 缺少H2）构成,这与哺乳类动物已知晶体结构的ERR_γ的配体结合区结构非常相似.pvERR氨基酸序列与其他昆虫ERRs氨基酸序列同源性很高,它与西方蜜蜂Apis mellifera雌激素相关受体amERR氨基酸序列相似性达到89.9 %;在进化关系上,pvERR与人类Homo sapiens ERRs的关系比果蝇Drosophila melanogaster雌激素相关受体dERR与人类的更近.本文可为进一步研究pvERR在昆虫发育中的功能提供有价值的信息.     

Structural studies on equine chorionic gonadotropin

The amino acid sequence of the subunit of equine chorionic gonadotropin (eCG, also pregnant mare serum gonadotropin, PMSG) has been determined. Overlapping peptides from tryptic and chymotrypic digests were isolated by a two-dimensional peptide mapping technique and sequenced by the Edman procedure. The proposed amino acid sequence of eCG is: (**Denotes carbohydrate attachment points.) This sequence differs significantly from that proposed by Rathnamet al. (1978) for equine follitropin subunit; in particular, their sequence lacked the first fourteen residues.For the subunit we have placed in sequence 104 amino acid residues by direct sequence determination and peptide overlap procedures; in addition, 37 residues have been placed provisionally by homology with the human chorionic gonadotropin (hCG) sequence and composition and/or sequence data for the peptides isolated in the present studies. Difficulties in the procurement of the hormone have stalled completion of the -subunit amino acid sequence determination. The data now available indicate that eCG -subunit is highly homologous to hCG subunit and the subunits of luteinizing hormone from the pituitary gland of the several species so far described. The proposed partial sequence of eCG is:     

Identification of a 24 kDa excretory secretory protein in Anisakis simplex

A gene coding for a 24 kDa protein (22 U homologous; As22U) was isolated from the Anisakis simplex third-stage larvae cDNA library during expressed sequence tag analysis. As22U was 636 bp long, and was found to code for 212 amino acid residues with a calculated mass of 23.5 kDa and a PI of 9.06. The As22U deduced amino acid sequence harbored a signal peptide region and 16 highly conserved cysteine residues, and it was identified in both the total extracts and excretory secretory (ES) protein of A. simplex. Its molecular weight was measured at 24 kDa via western blot analysis. The expression levels of thymic stromal lymphopoietin, IL-25, and CXCL1 (Gro-α) genes were increased at 6h after recombinant As22U treatment in mouse intestinal epithelial cells. Additionally, thymus and activation-regulated chemokine gene levels were increased at 14 h after treatment. Although we do not currently have sufficient evidence to determine whether As22U plays a role as an allergen, this remains possible. Further in vivo studies may provide some insight as to the allergenic properties of As22U.     

Isolation of the lipid-transporting protein Ns-LTP1 from seeds of the garden fennel flower (<Emphasis Type="Italic">Nigella sativa</Emphasis>)

A novel lipid-transporting protein (Ns-LTP1) has been isolated from seeds of the garden fennel flower Nigella sativa. The molecular mass, N-terminal amino acid sequence, and amino acid composition of the protein have been determined. Ns-LTP1 has a molecular mass of 9602 Da and contains eight cysteine residues which form four disulfide bridges. The protein is capable of suppressing the development of some phytopathogenic fungi and oomycetes.     

Human serum amyloid A (SAA): biosynthesis and postsynthetic processing of preSAA and structural variants defined by complementary DNA

To study structural variants of human serum amyloid A (SAA), an apoprotein of high-density lipoprotein, complementary DNA clones were isolated from a human liver library with the use of two synthetic oligonucleotide mixtures containing sequences that could code for residues 33-38 and 90-95 of the protein sequence. The SAA-specific cDNA clone (pA1) contains the nucleotide sequence coding for the mature SAA and 10 amino acids of the 18-residue signal peptide. It also includes a 70 nucleotide long 3'-untranslated region and approximately 120 bases of the poly(A) tail. The derived amino acid sequence of pA1 is identical with the alpha form of apoSAA1. A fragment of pA1 containing the conserved (residues 33-38) region of SAA also hybridized with RNA from human acute phase liver and acute phase stimulated, but not unstimulated, mouse and rabbit liver. In contrast, a fragment corresponding to the variable region hybridized to a much greater extent with human than with rabbit or murine RNA. Human acute phase liver SAA mRNA (approximately 600 nucleotides in length) directs synthesis of preSAA (Mr 14 000) in a cell-free translating system. In a Xenopus oocyte translation system preSAA is synthesized and processed to the mature Mr 12 000 product. The complete 18 amino acid signal peptide sequence of preSAA was derived from sequencing cDNA synthesized by "primer extension" from the region of SAA mRNA corresponding to the amino terminus of the mature product. Two other SAA-specific cDNA clones (pA6 and pA10) differed from pA1 in that they lack the internal PstI restriction enzyme site spanning residues 54-56 of pA1.(ABSTRACT TRUNCATED AT 250 WORDS)     

The primary structure of the human pancreatic secretory trypsin inhibitor: Amino acid sequence of the reduced S-aminoethylated protein

The amino acid sequence of human pancreatic secretory trypsin inhibitor [Pubols, M. H., Bartelt, D. C., and Greene, L. J. (1974) J. Biol. Chem., 249, 2235–2242] was determined by a combination of selective trypsin and chymotrypsin hydrolysis reactions on the S-2-aminoethylcysteinyl inhibitor and conventional methods (subtractive Edman degradation and exopeptidase hydrolysis) for sequence determination of small peptides. The peptides were ordered on the basis of the identification of the amino- and carboxyterminal residues of the products at each stage of the degradation procedure. The sequence determination was carried out on a mixture of chromatographic forms present in both tissue and pancreatic juice which are identical in amino acid composition, aminoterminal residues, molecular weight, and specific activity, but differ only in asparagine content and susceptibility to enzymatic hydrolysis. The amino acid sequence of the human inhibitor corresponding to chromatographic form A₃ has been shown to be NH₂

.     

Novel Bacillus thuringiensis δ-endotoxin active against Locusta migratoria manilensis

A novel δ-endotoxin gene was cloned from a Bacillus thuringiensis strain with activity against Locusta migratoria manilensis by PCR-based genome walking. The sequence of the cry gene was 3,432 bp long, and it encoded a Cry protein of 1,144 amino acid residues with a molecular mass of 129,196.5 kDa, which exhibited 62% homology with Cry7Ba1 in the amino acid sequence. The δ-endotoxin with five conserved sequence blocks in the amino-terminal region was designated Cry7Ca1 (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"EF486523","term_id":"1121787749","term_text":"EF486523"}}EF486523). Protein structure analysis suggested that the activated toxin of Cry7Ca1 has three domains: 227 residues forming 7 α-helices (domain I); 213 residues forming three antiparallel β-sheets (domain II); and 134 residues forming a β-sandwich (domain III). The three domains, respectively, exhibited 47, 44, and 34% sequence identity with corresponding domains of known Cry toxins. SDS-PAGE and Western blot analysis showed that Cry7Ca1, encoded by the full-length open reading frame of the cry gene, the activated toxin 1, which included three domains but without the N-terminal 54 amino acid residues and the C terminus, and the activated toxin 2, which included three domains and N-terminal 54 amino acid residues but without the C terminus, could be expressed in Escherichia coli. Bioassay results indicated that the expressed proteins of Cry7Ca1 and the activated toxins (toxins 1 and 2) showed significant activity against 2nd instar locusts, and after 7 days of infection, the estimated 50% lethal concentrations (LC₅₀s) were 8.98 μg/ml for the expressed Cry7Ca1, 0.87 μg/ml for the activated toxin 1, and 4.43 μg/ml for the activated toxin 2. The δ-endotoxin also induced histopathological changes in midgut epithelial cells of adult L. migratoria manilensis.     

A solitary human H3 histone gene on chromosome 1

A solitary histone H3 gene encoding a novel H3 protein sequence has been isolated. This H3 gene maps to chromosome 1 (1g42), whereas we have shown previously that the majority of the human histone genes form a large cluster on chromosome 6 (6p21.3). In addition, a small cluster has been described at 1q21. The clustered histone genes are expressed during the S-phase of the cell cycle, hence their definition as replication-dependent histone genes. In contrast, expression of replacement histone genes is essentially cell-cycle independent; they are solitary genes and map outside the major clusters. The newly described H3 gene maps outside all known histone gene clusters and varies by four amino acid residues from the consensus mammalian H3 structure. In contrast to other solitary histone genes, this human H3 gene shows the consensus promoter and 3 flanking portions that are typical for replication-dependent genes.     

Cloning and sequencing of a cDNA encoding ascorbate peroxidase fromArabidopsis thaliana

A cDNA clone encoding ascorbate peroxidase (AP, EC 1.11.1.11) was isolated from a phage gt11 library of cDNA fromArabidopsis thaliana by immunoscreening with monoclonal antibodies against the enzyme, and then sequenced. The cDNA insert hybridized to a 1.1 kb poly(A)⁺ RNA from leaves ofA thaliana. Genomic hybridization suggests that the cDNA obtained here corresponds to a single-copy gene. The N-terminal amino acid sequence ofArabidopsis AP was determined by protein sequencing of the immunochemically purified enzyme, and proved to be homologous to the N-terminal amino acid sequence of the chloroplastic AP of spinach. The predicted amino acid sequence of the mature AP ofA. thaliana, deduced from the nucleotide sequence, consists of 249 amino acid residues, which is 34% homologous with cytochromec peroxidase of yeast, but less homologous with other plant peroxidases. Amino acid residues at the active site of yeast cytochromec peroxidase are conserved in the amino acid sequence ofArabidopsis AP. The poly(dG-dT) sequence, which is a potential Z-DNA-forming sequence, was found in the 3 untranslated region of the cDNA.