Introduction of the cDNA for shape Arabidopsis glycerol-3-phosphate acyltransferase (GPAT) confers unsaturation of fatty acids and chilling tolerance of photosynthesis on rice

The chilling sensitivity of several plant species is closely correlated with the levels of unsaturation of fatty acids in the phosphatidylglycerol (PG) of chloroplast membranes. Plants with a high proportion of unsaturated fatty acids, such as Arabidopsis thaliana, are resistant to chilling, whereas species like squash with only a low proportion are rather sensitive to chilling. The glycerol-3-phosphate O-acyltransferase (GPAT) enzyme of chloroplasts plays an important role in determining the levels of PG fatty acid desaturation.A cDNA for oleate-selective GPAT of Arabidopsis under the control of a maize Ubiquitin promoter was introduced into rice (Oryza sativa L.) using the Agrobacterium-mediated gene transfer method. The levels of unsaturated fatty acids in the phosphatidylglycerol of transformed rice leaves were found to be 28% higher than that of untransformed controls. The net photosynthetic rate of leaves of transformed rice plants was 20% higher than that of the wild type at 17°C. Thus, introduction of cDNA for the Arabidopsis GPAT causes greater unsaturation of fatty acids and confers chilling tolerance of photosynthesis on rice.     

Mutagenesis of squash (Cucurbita moschata) glycerol-3-phosphate acyltransferase (GPAT) to produce an enzyme with altered substrate selectivity

In an attempt to rationalize the relationship between structure and substrate selectivity of glycerol-3-phosphate acyltransferase (GPAT, 1AT, EC 2.3.1.15) we have cloned a number of cDNAs into the pET overexpression system using a PCR-based approach. Following assay of the recombinant enzyme we noted that the substrate selectivity of the squash (Cucurbita moschata) enzyme had altered dramatically. This form of GPAT has now been crystallized and its full three-dimensional structure elucidated. Since we now have two forms of the enzyme that display different substrate selectivities this should provide a powerful tool to determine the basis of the selectivity changes. Kinetic and structural analyses are currently being performed to rationalize the changes which have taken place.     

甘油-3磷酸转酰酶氨基酸与植物抗冷性关系初探

甘油 - 3磷酸转酰酶 (GPAT)与植物抗冷性密切相关。南瓜 (Cucurbitamoschata)与黑子南瓜 (Cucurbitaficifolia)同属不同种 ,亲缘关系较近 ,但却存在显著的抗冷性差异。南瓜及黑子南瓜GPAT基因的克隆 ,可以使我们从二者推导的有限氨基酸的差异中对GPAT氨基酸组成及其与植物抗冷性作一定的探讨。发现在南瓜与黑子南瓜 13个不同的氨基酸残基中有 3个与抗冷性植物拟南芥菜 (Arabidopsisthaliana)、豌豆 (Pisumsativum)、红花 (Carthamustincto rius)和菠菜 (Spinaciaoleracea)等相同 ,可能与黑子南瓜比南瓜更具抗冷性的原因有关。比较南瓜、黑子南瓜、豌豆、红花、拟南芥菜和菠菜等植物中GPAT基因推导的氨基酸序列发现 ,在比较抗冷的拟南芥菜、红花、豌豆和菠菜等植物中 ,虽然它们之间的亲缘关系都比较远 ,但某些位点上的氨基酸残基却完全相同 ,而与南瓜等抗冷性较差的植物不同 ,这些位点的氨基酸残基可能也与GPAT对底物酰基的选择性有关。     

Identification of the polypeptides of the major light-harvesting complex of photosystem II (LHCII) with their genes in tomato.

Using an improved SDS-PAGE system, the polypeptides of the major chlorophyll a/b light-harvesting complex of PSII (LHCII) from tomato leaves were resolved into five polypeptide bands. All the polypeptides were matched with the genes encoding them by comparing amino acid sequences of tryptic peptides with gene sequences. The two major LHCII bands (usually comigrating as a '27 kDa' polypeptide) were encoded by cab1 and cab3 (Type I LHCII) genes. A third strong band of about 25 kDa was encoded by cab4 (Type II) genes. Polypeptides from two minor bands of 23-24 kDa were not N-terminally blocked; their N-terminal sequences showed they were Type III LHCII proteins. One complete cDNA clone and several incomplete clones for Type III polypeptides were sequenced. Combined with the peptide sequences, the results indicate that there are at least four different Type III genes in tomato, encoding four almost identical polypeptides. Thus, all the LHCII CAB polypeptides have been identified, and each type of LHCII polypeptide is encoded by distinct gene or genes in tomato.     

Two DNA sequences specific for the canine Y chromosome

Data are presented on the characterization of two nucleotide sequences found exclusively in the DNA of male dogs. In polymerase chain reactions (PCRs) of canine genomic DNA with a decanucleotide primer of arbitrary sequence (OP-W17), two nucleotide segments (650 and 990 bp) were amplified only from male samples, whereas a number of other fragments between 400 and 2500 bp in size were amplified from both male and female samples. The two male-specific segments were cloned and sequenced, and terminal 24mer oligonucleotide primer pairs were synthesized. PCR with these specific primer pairs resulted in amplification of the two male-specific sequences only from DNA samples of 34 male dogs; no product was amplified from 42 samples of females. A segment of the SRY gene previously localized on the Y chromosome could be amplified in DNA samples that had the two new sequences. Eco RI digested genomic male DNA when hybridized with the 650 bp or the 990 bp sequences, resulted in a single band for each on Southern analysis; DNA from females did not yield any bands. Comparisons between the two new sequences and the SRY gene segment revealed no homologies. We concluded that the two new sequences are specific for the canine Y chromosome and do not contain the short characterized segment of the SRY gene.     

黑子南瓜甘油-3-磷酸酰基转移酶基因的克隆及序列分析

依据国外报道的南瓜甘油－３－磷酸转酰酶（ＧＰＡＴ）基因的ｃＤＮＡ序列合成相应引物,用ＲＴ－ＰＣＲ技术,成功地分离了黑子南瓜（Ｃｕｃｕｒｂｉｔａｆｉｃｉｆｏｌｉａ）ＧＰＡＴ基因的ｃＤＮＡ片段,并亚克隆到了ｐＧＥＭ－Ｔ载体系统的多克隆位点上,序列分析表明黑子南瓜ＧＰＡＴ基因的ｃＤＮＡ序列及递推的氨基酸序列与南瓜（Ｃｕｃｕｒｂｉｔａｍｏｓｃｈａｔａ）相比分别具有９８％和９６５％的同源性。在１１８８ｂｐ中有２２个核苷酸发生变化,导致１３个氨基酸的改变     

毛头鬼伞中一条新28S rRNA的发现及其同源性分析

本研究从担子菌毛头鬼伞(Coprinus comatus)菌丝中分离获得一条新的28S rRNA序列,序列长度为906bp(GenBank accession No.GU568178)。该序列是我们前期在从毛头鬼伞中克隆一种烟草花叶病毒(TMV)的抗性蛋白基因y3时意外获得的一条非目的条带。将此获得的序列通过NCBI的BLAST,以及与其同源序列进行Clustal w和MEGA聚类分析,证实该序列是28S rRNA,同时还发现毛头鬼伞的系统进化关系比较离散。此外,在这一新28S rRNA与TMV的抗性蛋白基因y3之间发现有两个同源区段有可能是PCR扩增y3基因时出现非目的条带的原因。在这两个同源区段中,其一区段与克隆y3基因时所用的PCR引物之一有较高的相似性,另一区段也是一般PCR引物的类似物。本研究中新28S rRNA序列的获得是PCR扩增中出现非目的条带的新例,该序列的发现及聚类分析的结果有助于真菌基因组学研究及真菌生物分子分类系统的建立。     

Characterization of an angiotensin type-1 receptor partial cDNA from rat kidney: evidence for a novel AT1B receptor subtype.

We sought to determine if multiple forms of mRNA for the angiotensin type-1 (AT1) receptor could be detected in rat kidney using the polymerase chain reaction (PCR) procedure. Amplification of rat kidney cDNA with oligonucleotide primers derived from the second and sixth transmembrane domains of the rat AT1 receptor yielded a single cDNA fragment 528bp in size. Sequence analysis indicated, however, that the cDNA fragment was a mixture of two highly similar gene products: the first cDNA was identical to the previously cloned AT1 receptor (termed here AT1A) whereas the second cDNA (termed here AT1B) was 92% identical at the nucleotide level and 96% identical at the amino acid level. Nucleotide substitutions were dispersed throughout the cDNA and 80% (33 of 41) were conservative. Significant levels of AT1A and AT1B mRNA were detected by PCR amplification of kidney poly(A)+ RNA and restriction enzyme analysis. These results indicate that at least two distinct AT1 receptor genes are expressed in rat kidney.     

Miniprimer PCR, a New Lens for Viewing the Microbial World

Molecular methods based on the 16S rRNA gene sequence are used widely in microbial ecology to reveal the diversity of microbial populations in environmental samples. Here we show that a new PCR method using an engineered polymerase and 10-nucleotide “miniprimers” expands the scope of detectable sequences beyond those detected by standard methods using longer primers and Taq polymerase. After testing the method in silico to identify divergent ribosomal genes in previously cloned environmental sequences, we applied the method to soil and microbial mat samples, which revealed novel 16S rRNA gene sequences that would not have been detected with standard primers. Deeply divergent sequences were discovered with high frequency and included representatives that define two new division-level taxa, designated CR1 and CR2, suggesting that miniprimer PCR may reveal new dimensions of microbial diversity.     

Association of Phosphatidylcholine with Soybean 11S Globulin

To address the multiplicity of aromatic ring hydroxylation dioxygenases, we used PCR amplification and denaturing gradient gel electrophoresis (DGGE). The amplified DNA fragments separated into five bands, A to E. Southern hybridization analysis of RHA1 total DNA using the probes for each band showed that band C originated from a couple of homologous genes. The nucleotide sequences of the bands showed that bands A, C, and E would be parts of new dioxygenase genes in RHA1. That of band B agreed with the bphA1 gene, which was characterized previously. That of band D did not correspond to any known gene sequences. The regions including the entire open reading frames (ORFs) were cloned and sequenced. The nucleotide sequences of ORFs suggested that the genes of bands A,C, and E may respectively encode benzoate, biphenyl, and polyhydrocarbon dioxygenases. Northern hybridization indicated the induction of the gene of band A by benzoate and biphenyl, and that of the gene of band C by biphenyl and ethylbenzene, supporting the above notions. The gene of band E was not induced by any of these substrates. Thus the combination of DGGE and Southern hybridization enable us to address the multiplicity of the ring hydroxylation dioxygenase genes and to isolate some of them.     

Multiplicity of aromatic ring hydroxylation dioxygenase genes in a strong PCB degrader, Rhodococcus sp. strain RHA1 demonstrated by denaturing gradient gel electrophoresis

To address the multiplicity of aromatic ring hydroxylation dioxygenases, we used PCR amplification and denaturing gradient gel electrophoresis (DGGE). The amplified DNA fragments separated into five bands, A to E. Southern hybridization analysis of RHA1 total DNA using the probes for each band showed that band C originated from a couple of homologous genes. The nucleotide sequences of the bands showed that bands A, C, and E would be parts of new dioxygenase genes in RHA1. That of band B agreed with the bphA1 gene, which was characterized previously. That of band D did not correspond to any known gene sequences. The regions including the entire open reading frames (ORFs) were cloned and sequenced. The nucleotide sequences of ORFs suggested that the genes of bands A, C, and E may respectively encode benzoate, biphenyl, and polyhydrocarbon dioxygenases. Northern hybridization indicated the induction of the gene of band A by benzoate and biphenyl, and that of the gene of band C by biphenyl and ethylbenzene, supporting the above notions. The gene of band E was not induced by any of these substrates. Thus the combination of DGGE and Southern hybridization enable us to address the multiplicity of the ring hydroxylation dioxygenase genes and to isolate some of them.     

Purification and cDNA sequencing of an oleate-selective acyl-ACP:sn-glycerol-3-phosphate acyltransferase from pea chloroplasts

The soluble acyl-ACP:sn-glycerol-3-phosphate acyltransferase from chloroplasts of chilling-sensitive and -resistant plants differ in their fatty acid selectivity. Enzymes from resistant plants discriminate against non-fluid palmitic acid and select oleic acid whereas the acyltransferase from sensitive plants accepts both fatty acids. To use this difference for improving plant chilling resistance by biotechnology the gene for an oleate-selective enzyme is required. Therefore, the oleate-selective enzyme from pea seedlings was purified to apparent homogeneity. Tryptic peptides of internal origin were sequenced. Polyclonal antibodies raised in rabbits were used for an immunological screening of a pea leaf cDNA expression library in gt11. A positive clone of 1800 bp was selected showing an open reading frame which codes for 457 amino acids. The deduced amino acid sequence coincides perfectly with the tryptic sequences. A tentative assignment of the processing site was made which divides the preprotein into a mature protein of 41 kDa in accordance with experimental findings and a transit peptide of 88 amino acids. At present the comparison between a selective (pea) and an unselective (squash) acyltransferase sequence does not provide a clue for recognizing the structural differences resulting in different selectivities.     

Separation of bacteria of the Clostridium leptum subgroup from the human colonic microbiota by fluorescence-activated cell sorting or group-specific PCR using 16S rRNA gene oligonucleotides

Molecular methods based on 16S rRNA gene sequence analyses have shown that bacteria of the Clostridium leptum subgroup are predominant in the colonic microbiota of healthy humans; this subgroup includes bacteria that produce butyrate, a source of energy for intestinal epithelial cells. To improve our understanding of the species within this important group, separation methods using fluorescence-activated cell sorting (FACS) and specific PCR were combined with 16S rRNA gene sequence analyses. FACS was developed for bacteria labelled in situ with two rRNA oligonucleotide probes, namely EUB338-FITC for total bacteria and Clep866-CY5/cp or Fprau645-CY5 for bacteria of the C. leptum subgroup. Bacterial cell sorting allowed a selective recovery of members of the C. leptum subgroup from the human microbiota with efficiencies as high as 95%. Group-specific PCR amplification of the C. leptum subgroup was developed, and temporal thermal gradient gel electrophoresis showed host-specific profiles with low complexity, with a sharing of common bands between individuals and bands stable over 2 months for the same individual. A library of 16S rRNA gene cloned sequences (106 sequences) was prepared with DNA obtained from both separation methods, and 15 distinct phylotypes were identified, among which 10 have no cultivable or currently cultivated representative in reference collections.     

野生罂粟COR、BBE基因片段融合及其RNAi载体构建

可待因酮还原酶(COR)与小檗碱桥酶(BBE)是吗啡合成代谢途径的关键酶,其活性大小直接影响着吗啡合成途径中生物碱的代谢合成。采用RT-PCR从罂粟幼叶克隆出COR和BBE基因全序列,同源性比较结果显示,它们与GenBank上已报道的COR和BBE基因高度同源。利用blast及分子生物学软件DNAStar对COR和BBE基因的cDNA序列同源性进行分析比较,分别从各基因中筛选和克隆了一段同源性极低、约400～500 bp的片段;并应用重叠PCR法将其拼接成744 bp的融合基因BC,以中间载体pHANNIBAL和植物表达载体pART27为基础,构建了以CaMV 35S启动子驱动的含有“正向BC融合片段- pdk内含子-反向BC融合片段”的ihRNAi植物表达载体,通过转化野生罂粟,初步研究了以COR和BBE基因为靶标的RNAi对内源吗啡合成的抑制效果,为进一步培育低吗啡高蒂巴因的罂粟种质提供了依据。     

Identification of the Hind III polymorphic site in the PAI-1 gene: analysis of the PAI-1 Hind III polymorphism by PCR

The identification of the Hind III polymorphic site in the 3' end of the plasminogen activator inhibitor 1 (PAI-1) gene and a simple method to identify the Hind III polymorphism rapidly in the PAI-1 gene using PCR is described. The Hind III restriction site was identified by restriction site mapping and sequence analysis from a cosmid DNA clone. Genomic DNA was isolated from individual human umbilical cords and a 754-bp fragment of the human PAI-1 gene was amplified by PCR. Aliquots of the PCR products were digested with Hind III and analyzed by agarose gel electrophoresis. The presence of two fragments, 754 and 567 bp, was identified, and they were designated as 1/1 (750-bp band), 1/2 (754- and 567-bp bands), and 2/2 (567-bp band). The PCR method is considerably less time consuming than the conventional DNA genotyping using Southern blot analysis. To ensure that this new method identified the same PAI-1 genotypes as previously identified by Hind III restriction fragment length polymorphism (RFLP), samples were simultaneously genotyped by PCR and Southern blot analysis. Both methods identified the same Hind III genotypes in all the samples, confirming the reliability of this new PCR method for the rapid identification of the Hind III polymorphism in the human PAI-1 gene.