Characterization of the chromosomal aac(6'')-Ic gene from Serratia marcescens.

The DNA sequence of the chromosomal aac(6')-Ic gene from Serratia marcescens, which had been previously cloned (H. M. Champion, P. M. Bennett, D. A. Lewis, and D. S. Reeves, J. Antimicrob. Chemother. 22:587-596, 1988) was determined. High-pressure liquid chromatographic analysis of extracts prepared from Escherichia coli carrying the chromosomal aac(6')-Ic gene on a plasmid confirmed the presence of 6'-N-acetyltransferase activity in this strain, which was suggested by the aminoglycoside resistance profile. DNA sequence analysis of the cloned 2,057-bp PstI fragment revealed several regions of homology to previously characterized sequences from GenBank, including the rpoD and tRNA-2 genes of E. coli. Subcloning experiments confirmed the coding sequence of the aac(6')-Ic gene to be at positions 1554 to 1992. The predicted amino acid sequence of the AAC(6')-Ic protein suggested that it was the third member of a family of AAC(6') proteins which included a coding region identified between the aadB and aadA genes of Tn4000 and an AAC(6') protein encoded by pUO490, which was isolated from Enterobacter cloacae. Primer extension analysis suggested that the -35 region of the aac(6')-Ic promoter overlapped a large palindromic sequence which may be involved in the regulation of the aac(6')-Ic gene. Hybridization experiments utilizing a restriction fragment from the aac(6')-Ic gene showed that all S. marcescens organisms carried this gene whether or not the AAC(6')-I resistance profile was expressed. Organisms other than Serratia spp. did not hybridize to this probe.     

Molecular cloning and characterization of the vasopressin-regulated urea transporter of rat kidney collecting ducts.

Absorption of urea in the renal inner medullary collecting duct (IMCD) contributes to hypertonicity in the medullary interstitium which, in turn, provides the osmotic driving force for water reabsorption. This mechanism is regulated by vasopressin via a cAMP-dependent pathway and activation of a specialized urea transporter located in the apical membrane. We report here the cloning of a novel urea transporter, designated UT1, from the rat inner medulla which is functionally and structurally distinct from the previously reported kidney urea transporter UT2. UT1 expressed in Xenopus oocytes mediated passive transport of urea that was inhibited by phloretin and urea analogs but, in contrast to UT2, was strongly stimulated by cAMP agonists. Sequence comparison revealed that the coding region of UT1 cDNA contains the entire 397 amino acid residue coding region of UT2 and an additional 1,596 basepair-stretch at the 5' end. This stretch encodes a novel 532 amino acid residue NH2-terminal domain that has 67% sequence identity with UT2. Thus, UT1 consists of two internally homologous portions that have most likely arisen by gene duplication. Studies of the rat genomic DNA further indicated that UT1 and UT2 are derived from a single gene by alternative splicing. Based on Northern analysis and in situ hybridization, UT1 is expressed exclusively in the IMCD, particularly in its terminal portion. Taken together, our data show that UT1 corresponds to the previously characterized vasopressin-regulated urea transporter in the apical membrane of the terminal IMCD which plays a critical role in renal water conservation.     

Cloning, sequencing, and use as a molecular probe of a gene encoding an aminoglycoside 6''-N-acetyltransferase of broad substrate profile.

A gene coding for an aminoglycoside 6'-N-acetyltransferase that was able to modify amikacin was cloned from a plasmid isolated from a clinical strain of Enterobacter cloacae. Sequencing of a 955-bp segment which mediates the modifying activity revealed a single open reading frame of 432 nucleotides that predicted a polypeptide of 144 amino acid residues with a molecular weight of 16,021. Putative ribosomal binding sites and -10 and -35 sequences were located at the 5' end of the gene. The size of the polypeptide was confirmed through minicell analysis of the expression products of plasmids containing the sequence. The use of the gene as a molecular probe revealed its specificity toward strains harboring genes coding for related enzymes. This probe is therefore useful for epidemiological studies.     

A muscle-specific actin gene from the Mediterranean fruit fly, Ceratitis capitata

A characterization of an actin gene isolated from the genome of the Mediterranean fruit fly, Ceratitis capitata , including the complete sequencing of the coding, 3' and 5' flanking regions of this gene and a partial cDNA was carried out. The partial cDNA was derived from the 3' untranslated region of the actin gene described here, and has been used to identify this gene uniquely. The DNA sequence data presented here, together with the pattern of expression exhibited by this gene during development, strongly support the interpretation that this is a muscle-specific actin gene. Peaks of expression are seen in tissues and during temporal phases of development where muscle differentiation is occurring. The derived protein sequence of the Medfly actin gene shows the highest degrees of similarity, 98.4 and 96.6% respectively, with the two muscle-specific actin genes 79B and 88F from D. melanogaster . The Medfly actin gene also has a single intervening sequence, and an intron is found at the same position in the 79B and 88F actin genes. In the coding region at the DNA level, 17.2 and 16.4% nucleotide differences, respectively, are observed between the Medfly actin gene and these same two D. melanogaster actin genes. The disparity between the amino acid and nucleotide comparisons can be explained, in part, by a high level of synonymous changes in the DNA sequence. In addition, despite the many similarities, codon usage appears to be very different between the actin genes of these species.     

Revised analysis of aadA2 gene of plasmid pSa.

The nucleotide sequence of gene aadA2 of plasmid pSa, coding for aminoglycoside-3"-adenyltransferase, has been reexamined. We found differences with respect to the sequence previously determined by Tait et al. (R. C. Tait, H. Rempel, R. L. Rodriguez, and C. I. Kado, Gene 36:97-104, 1985). These deviations are located in the coding region and in the 3' noncoding region. By making deletions in the region for initiation of protein synthesis, we identified a GTG triplet as the most probable start codon for translation.     

Characterization of Acinetobacter haemolyticus aac(6')-Ig gene encoding an aminoglycoside 6'-N-acetyltransferase which modifies amikacin.

The amikacin resistance gene acc(6')-Ig of Acinetobacter haemolyticus BM2685 encoding an aminoglycoside 6'-N-acetyltransferase was characterized. The gene was identified as a coding sequence of 438 bp corresponding to a protein with a calculated mass of 16,522 Da. Analysis of the deduced amino acid sequence suggested that it was the fourth member of a subfamily of aminoglycoside 6'-N-acetyltransferases. The resistance gene was not transferable either by conjugation to Escherichia coli or to Acinetobacter baumannii or by transformation into Acinetobacter calcoaceticus. Plasmid DNA from strain BM2685 did not hybridize with an intragenic aac(6')-Ig probe. These results suggest a chromosomal location for this gene. The gene was detected by DNA hybridization in all 20 strains of A. haemolyticus tested but not in 179 other Acinetobacter strains, including A. baumannii, A. lwoffii, A. junii, and A. johnsonii and genospecies 3, 6, 11, 13, 14, 15, 16, and 17, of which 162 were amikacin resistant. The probe did not hybridize in dot blot assays with DNAs purified from members of the families Enterobacteriaceae and Pseudomonadaceae that encode 6'-N-acetyltransferases. These data suggest that the aac(6')-Ig gene is species specific and may be used to identify A. haemolyticus.     

Development of a DNA probe from the deoxyribonucleotide sequence of a 3-N-aminoglycoside acetyltransferase [AAC(3)-I] resistance gene.

The aacC1 gene encoding the 3-N-aminoglycoside acetyltransferase [AAC(3)-I] was cloned from enteric plasmid pJR88, and its deoxyribonucleotide sequence was determined. Significant nucleotide homology was noted in the region extending from the proposed -35 sequences through the first 59 base pairs of the aacC1 gene open reading frame (ORF) and the upstream flanking regions and ORFs of several other antibiotic resistance genes. Sequences were noted to be homologous with the 6'-N-aminoglycoside acetyltransferase [AAC(6')-I], 2'-O-aminoglycoside adenylyltransferase [AAD(2')], and 3'-O-aminoglycoside adenylyltransferase [AAD(3')] resistance genes; the OXA-1, OXA-2, and PSE-2 beta-lactamase genes; and several dihydrofolate reductase genes. Small regions of homology were noted in the 3'-flanking regions of these resistance genes as well. A DNA probe for the aacC1 gene was selected from the nucleotide sequence information and was tested against a series of genetically and enzymatically defined strains. The probe, which proved specific for the aacC1 gene, was then tested against a series of 58 gentamicin-susceptible and 219 gentamicin-resistant gram-negative bacilli isolated from patients at the Seattle Veterans Administration Medical Center. Only six clinical isolates were noted to carry the aacC1 gene. Each was resistant to gentamicin but susceptible to kanamycin, tobramycin, and amikacin. The presence of homologous regions of DNA at both the 3' and 5' ends of the aacC1 gene reinforces the importance of choosing probes from within the ORFs of genes and of avoiding flanking sequences. When the homology with other sequences extends into the ORF, as it does with the aacC1 gene, development of a specific probe may require determination of the nucleotide sequence.     

Human J chain gene. Structure and expression in B lymphoid cells

As part of an ongoing investigation of the regulation of gene expression in B cell development, we have obtained a genomic DNA clone encoding the human J chain protein. The nucleotide sequence of exons encoding the mature protein defines a 137 amino acid primary sequence similar to that previously determined at the protein level. Probes from the gene have been used to analyze J chain expression in human cell lines corresponding to pre-B and B lymphocytes. J chain RNA was detected in two of six human pre-B cell lines and in 8 of 10 B cell lines expressing various Ig isotypes. The expression of the J chain gene is, thus, not tightly linked to IgM or IgA secretion. Our data do not, however, support the recent suggestion (7) that synthesis of J chain precedes that of mu chain in B lymphocyte differentiation. Because of the presence of nine candidate polyadenylation signals (AATAAA or AATTAAA) downstream of the C-terminal coding block of the J chain gene, the 3' end of the gene could not be determined from sequence data alone. To define the 3' end, J chain RNA from a human B lymphocyte line was used to protect an end-labelled DNA fragment from S1 nuclease digestion. The sequence 40 basepairs 5' of the functional polyadenylation site identified by these S1 experiments is homologous the same region of a previously reported mouse J chain complementary DNA clone.     

Isolation, characterization, and DNA sequence analysis of an AAC(6'')-II gene from Pseudomonas aeruginosa.

The gene encoding a 6'-N-acetyltransferase, AAC(6')-II, was cloned from Pseudomonas aeruginosa plasmid pSCH884. This gene mediates resistance to gentamicin, tobramycin, and netilmicin but not amikacin or isepamicin. The DNA sequence of the gene and flanking regions was determined. The 5'- and 3'-flanking sequences showed near identity to sequences found abutting a variety of different genes encoding resistance determinants. It is likely that the current structure arose by the integration of the 572-base-pair sequence containing the AAC(6')-II gene into a Tn21-related sequence at the recombinational hot spot, AAAGTT. We have compared the sequence of the AAC(6')-II gene to genes of other 6'-N-acetyltransferases. An AAC(6')-Ib protein (encoded by the aacA4 gene; G. Tran Van Nhieu and E. Collatz, J. Bacteriol. 169:5708-5714, 1987) that results in resistance to amikacin but not gentamicin was found to share 82% sequence similarity with the AAC(6')-II protein. We speculate that these two genes arose from a common ancestor and that the processes of selection and dissemination have led to the observed differences in the spectrum of aminoglycoside resistance.     

PCR法分子克隆及序列分析广西产眼镜王蛇蛇毒α-神经毒素基因

目的 为了获得眼镜王蛇(ophiophagus hannah，Oh)蛇毒a-神经毒素(a-Neurotoxin．a-NT)的基因序列。方法 我们通过比较了基因库中已知眼镜蛇科不同种类毒蛇来源的a-NT基因，发现它们有较高的同源性，特别是5’和3’非翻译区及引导肽部分高度保守，据此设计了包括翻译起始点的上游引物，以及为了得到3’端较完整非编码部分而设计了基本上属于d(T)的反意链下游RACE-PCR引物。为了克服引物所带来的模糊扩增，还在蛋白编码部分再设计一对上下游引物，由此组成P1、P2、P3和P4四对引物。采用Nacleospin RNA Kit法分别从3条活Oh蛇毒腺中提取mRNA，以3’端引物合成eDNA的第一链，并以此作为模板，分别用四对引物进行PCR扩增反应，得到了目的基因不同长度的PCR产物，产物经精制后进行测序，对比分析其结果。结果 获得了全长474bp的Oh．eDNA的基因核苷酸序列，包括5’端60bp，信号肽伴启动子ATG63bp，蛋白质密码部分216bp和3’端186bp并含有TGA终止码。经基因库信息计算机分析其信号肽与眼镜蛇树属(Pseudonnaja textilis，Pt．)海蛇(Laticauda semufasciata，Ls)100％同源，96.8％与眼镜蛇南洋亚种(Naja sputatrix，Ns)和银环蛇(Bungarus multicinctus，Bm)同源．蛋白密码部分83.3％与Ns，79.2％与Pt，76.4％与Ls和74.1％与Bm同源．氨基酸顺序分析信号肽后紧接着的72个氨基酸90.3％与已发现的眼镜王蛇毒长链a—NT’toxina同源，大约73．6％Toxinb、69．7％Oh-4、66.7％Oh-5、56.9％Oh-6A和6B同源，并与a-银环蛇毒素54.2％同源。结论 新发现的Oh-eDNA属于长链a-NT的基因。     

Reconstitution of human Fc gamma RIII cell type specificity in transgenic mice

The human low affinity receptors for the Fc domain of immunoglobulin G, Fc gamma RIII, are encoded by two genes (IIIA and IIIB) which share >95% sequence identity in both coding and flanking sequences. Despite this extraordinary sequence conservation, IIIA is expressed in natural killer (NK) cells and macrophages and is absent in neutrophils, whereas IIIB is expressed only in neutrophils. To determine the molecular basis for this differential expression, we have generated transgenic mice using the genomic sequences of IIIA and IIIB. IIIA and IIIB transgenic mice show faithful reconstitution of this human pattern of cell type specificity. To determine the cis acting sequence elements that confer this specificity, we constructed chimeric genes in which 5.8 kb of 5' sequences of the IIIB gene has been replaced with a homologous region from the IIIA gene, and conversely, IIIA 5' sequences have been substituted for the analogous region of the IIIB gene. Promoter swap transgenic mice that carry IIIA 5' flanking sequences express Fc gamma RIII in macrophages and NK cells. In contrast, promoter swap transgenic mice that contain IIIB 5' sequences express Fc gamma RIII in neutrophils only. These studies define the elements conferring the cell type-specific expression of the human Fc gamma RIII genes within the 5' flanking sequences and first intron of the human Fc gamma RIIIA and Fc gamma RIIIB genes.     

Mutation of the signal peptide-encoding region of the preproparathyroid hormone gene in familial isolated hypoparathyroidism.

Preproparathyroid hormone (preproPTH) gene mutation has been proposed as a cause of familial isolated hypoparathyroidism (FIH). We cloned the preproPTH alleles of a patient with autosomal dominant FIH and sequenced the coding regions, 5' flanking regions, and splice junctions. The putatively abnormal (based on previous linkage studies) allele differed from the other allele's normal sequence at only one nucleotide. This T to C point mutation changes the codon for position 18 of the 31 amino acid prepro sequence from cysteine to arginine, disrupting the hydrophobic core of the signal sequence. Because the hydrophobic core is required by secreted proteins for efficient translocation across the endoplasmic reticulum, the mutant protein is likely to be inefficiently processed. Indeed, in vitro studies demonstrated dramatically impaired processing of the mutant preproPTH to proPTH. In summary, we observed a point mutation in the signal peptide-encoding region of a preproPTH gene in one FIH kindred and demonstrated a functional defect caused by the mutation. Mutation of the signal sequence constitutes a novel pathophysiologic mechanism in man, and further study may yield important insights both into this form of hormone deficiency and into the role of signal sequences in human physiology.     

IgA肾病患者β1，3-半乳糖基转移酶特异性伴侣蛋白Cosmc基因编码区的序列分析

背景:IgA肾病发病机制迄今不明,目前研究证实IgA肾病患者IgA1分子铰链区β1,3-半乳糖基转移酶的活性降低引起IgA1分子O-糖基化异常是该病发生的重要途径。作者前期研究推测IgA肾病患者外周血B淋巴细胞β1,3-半乳糖基转移酶特性伴侣蛋白Cosmc表达降低可能是IgA肾病糖基化异常原因的中心环节。目的:检测IgA肾病患者β1,3-半乳糖基转移酶特异性伴侣蛋白Cosmc基因编码区的DNA序列,并与Gene Bank公布的序列比对。设计:病例-对照观察。单位:四川大学华西医院肾内科。对象:选择2005-11/2006-08四川大学华西医院肾内科收治的肾病患者37例,包括IgA肾病患者27例和非IgA肾病患者10例,另选择5例健康自愿者,所有观察对象均知情同意。方法:实验于四川大学生物治疗国家重点实验室完成。采集所有观察对象的肝素钠抗凝外周静脉血2mL,采用经典酚氯仿法提取外周血基因组DNA,应用紫外分光光度仪定量DNA的含量,应用聚合酶链反应扩增所有观察对象的β1,3-半乳糖基转移酶特异性伴侣蛋白Cosmc基因编码区,并对每个观察对象的聚合酶链反应产物进行直接测序,将所有测序结果分别与GeneBank公布序列一一进行比对。主要观察指标:β1,3-半乳糖基转移酶特异性伴侣蛋白Cosmc基因编码区的聚合酶链式反应产物扩增结果及测序序列。结果:①Cosmc基因的编码区位于Cosmc基因的257-1213位,扩增后的Cosmc基因大小为1247bp。②IgA肾病患者、非IgA肾病患者以及健康自愿者之间的β1,3-半乳糖基转移酶特异性伴侣蛋白Cosmc基因编码区序列均一致,并与GeneBank公布的序列无差异。结论:未发现IgA肾病患者有Cosmc基因编码区序列异常,提示Cosmc基因编码区序列与IgA肾病IgA1分子的糖基化异常可能无关。     

Identification and function of Abdominal-A in the silkworm, Bombyx mori

Abdominal-A ( adb-A ) is a key gene in the development of insects. To understand its function in the silkworm, we cloned 1193 bp of the abd-A gene of Bombyx mori ( Bmabd-A ), including the complete coding sequence and part of the 3' untranslated region sequence. Bmabd-A has at least three mRNA splice variants with coding sequences of lengths 1032, 1044 and 1059 bp, encoding 343, 347 and 352 amino acids, respectively. Each splice variant of Bmabd-A has three exons and differs only in second exon size. Bmabd-A was expressed at low levels in unfertilized eggs, but increased gradually in fertilized eggs after laying 22 h. Bmabd-A expression decreased in ant silkworms (newly hatched silkworms). After RNA interference for Bmabd-A , the embryos had two mutant phenotypes, either completely or partially absent abdominal feet from the third to sixth abdominal segments, suggesting that Bmabd-A is responsible for normal development of the third to sixth abdominal segments during embryonic development.