The Human CYP2C Locus: A Prototype for Intergenic and Exon Repetition Splicing Events

In human there are four known CYP2C genes that have been mapped to chromosome 10q24 with the order Cen–2C18–2C19–2C9–2C8–Tel. Previously we have shown that splicing events joining exons from the neighboring 2C18 and 2C19 genes occur in human liver and epidermis. Here evidence is presented that the terminal genes of this cluster, 2C18 and 2C8, are also involved in intergenic splicing. Most interestingly, several of these 2C18/2C8 RNAs were composed of all nine exons, thus conceivably having the potential for coding functional proteins. Moreover, chimeric RNA species consisting of exons originating not only from the CYP2C8 and CYP2C18 genes, but also from the CYP2C19 gene were detected. In all cases the exons from the different CYP2C genes were joined at the correct canonical splice sites. However, the closely linked RBP4 gene is not participating in intergenic splicing with the CYP2C genes. In addition, CYP2C8 gene expression was found to generate a variety of scrambled RNA molecules including species that contained repetitions of certain exons.     

Analysis of the Promoter of the Auxin-Inducible Gene, parC, of Tobacco

The auxin-responsive region (AuxRR) in the promoter of the parCgene was analyzed in transgenic tobacco plants in which the5' flanking region of the parC promoter was placed upstreamof the gene for rß-glucuronidase (GUS). The AuxRRwas located between nucleotides (nt) –226 and –54.Detailed dissection of this segment revealed that the presenceof the non-contiguous sequences from nt –226 to –151and from nt –84 to –54 was required for the expressionof the auxin responsiveness of the parC promoter. The sequencefrom nt –226 to –151 was found to contain a sequencewhich resembles the as-1 element in the 35S promoter of cauliflowermosaic virus (CaMV). Although it has been reported that theas-1 element is involved in auxin responsiveness [Liu and Lam(1994) J. Biol. Chem. 269: 668], we showed that introductionof a point mutation into the as-1-like sequence completely eliminatedauxin responsiveness, a result that suggests that the sequenceis indispensable for auxin responsiveness. However, the presenceof the as-1-like sequence alone was not sufficient for auxinresponsiveness, since the segment (nt –226 to –84)that included the as-1-like sequence failed to confer auxinresponsiveness on the core promoter. It is possible that thetwo separately located sequences play specific roles in interactionswith trans-factors that are required for the expression of theauxin responsiveness of the parC promoter. (Received March 11, 1996; Accepted July 9, 1996)     

Photosynthetic Characteristics of C3-C4 Intermediate Flaveria Species II. Kinetic Properties of Phosphoenolpyruvate Carboxylase from C3, C4 and C3-C4 Intermediate Species

The kinetic properties of phosphoenolpyruvate (PEP) carboxylasehave been studied among several Flaveria species: the C₃ speciesF. cronquistii, the C₃–C₄ species F. pubescens and F.linearis, and the C₄ species F. trinervia. At either pH 7 or8, the maximum activities (in µmol.mg Chl^–1.h^–1)for F. pubescens and linearis (187–513) were intermediateto those of the C₃ species (12–19) and the C₄ species(2,182–2,627). The response curves of velocity versusPEP concentration were hyperbolic for the C₃ and C₃–C₄species at either pH 7 or 8 while they were sigmoidal for theC₄ species at pH 7 and hyperbolic at pH 8. The K_m values forPEP determined from reciprocal plots were lowest in the C₃ species,and of intermediate value in the C₃–C₄ species comparedto the K' values of the C₄ species determined from Hill plotsat either pH 7 or 8. Glucose-6-phosphate (G6P) decreased theK_m values for PEP at both pH 7 and 8 in the C₃ and C₃–C₄species. In the C₄ species, G6P decreased the K' values at pH8 but increased the K' values at pH 7. In all cases, G6P hadits effect by influencing the activity at limiting PEP concentrationswith little or no effect on the maximum activity. At pH 8 andlimiting concentrations of PEP the degree of stimulation ofthe activity by G6P was greatest in the C₄ species, intermediatein F. linearis, a C₃–C₄ species, and lowest in the C₃species. In several respects, the PEP carboxylases of the C₃–C₄Flaveria species have properties intermediate to those of theC₃ and C₄ species. (Received April 30, 1983; Accepted August 22, 1983)     

Carbon Exchange Rate of Intact Individual Soya Bean Pods. 2. Ontogeny of Temperature Sensitivity

Diurnal temperature fluctuations induced change in soya bean-pod[Glycine max (L.) Merr.] carbon exchange rate (CER, where positiveCER represents CO₂ evolution). CER appeared to depend linearlyon temperature. Linear regressions of CER on temperature interceptedthe temperature axis at 5°C (i.e. zero CER at 5°C).Slopes of these regressions (i.e. temperature sensitivity) changedover the season. The CER-temperature sensitivity coefficient,K, (calculated from observed values of CER. pod temperatureand temperature intercept) rose from less than 0·02 mgCO₂ h^–1 pod^–1 °C^–1 during early pod-flll,peaked at over 0·04 mg CO₂ h^–1 pod^–1 °C^–1at mid pod-fill, and then declined during late pod-fill andmaturation. Glycine max (L.) Merr., Soya bean, carbon exchange rate, temperature     

Biochemical Limitations to Carbon Assimilation in C3 Plants--A Retrospective Analysis of the A/Ci Curves from 109 Species

Species-specific differences in the assimilation of atmosphericCO₂ depends upon differences in the capacities for the biochemicalreactions that regulate the gas-exchange process. Quantifyingthese differences for more than a few species, however, hasproven difficult. Therefore, to understand better how speciesdiffer in their capacity for CO₂ assimilation, a widely usedmodel, capable of partitioning limitations to the activity ofribulose-1,5-bisphosphate carboxylase-oxygenase, to the rateof ribulose 1,5-bisphosphate regeneration via electron transport,and to the rate of triose phosphate utilization was used toanalyse 164 previously published A/C_i, curves for 109 C₃ plantspecies. Based on this analysis, the maximum rate of carboxylation,Vc_max, ranged from 6µmol m^–2 s^–1 for the coniferousspecies Picea abies to 194µmol m^–2 s^–1 forthe agricultural species Beta vulgaris, and averaged 64µmolm^–2 s^–1 across all species. The maximum rate ofelectron transport, J_max, ranged from 17µmol m^–2s^–1 again for Picea abies to 372µmol m^–2 s^–1for the desert annual Malvastrum rotundifolium, and averaged134µmol m^–2 s^–1 across all species. A strongpositive correlation between Vc_max and J_max indicated that theassimilation of CO₂ was regulated in a co-ordinated manner bythese two component processes. Of the A/C_i curves analysed,23 showed either an insensitivity or reversed-sensitivity toincreasing CO₂ concentration, indicating that CO₂ assimilationwas limited by the utilization of triose phosphates. The rateof triose phosphate utilization ranged from 4·9 µmolm^–2 s^–1 for the tropical perennial Tabebuia roseato 20·1 µmol m^–2 s^–1 for the weedyannual Xanthium strumarium, and averaged 10·1 µmolm^–2 s^–1 across all species. Despite what at first glance would appear to be a wide rangeof estimates for the biochemical capacities that regulate CO₂assimilation, separating these species-specific results intothose of broad plant categories revealed that Vc_max and J_maxwere in general higher for herbaceous annuals than they werefor woody perennials. For annuals, Vc_max and J_max averaged 75and 154 µmol m^–2 s^–1, while for perennialsthese same two parameters averaged only 44 and 97 µmolm^–2 s^–1, respectively. Although these differencesbetween groups may be coincidental, such an observation pointsto differences between annuals and perennials in either theavailability or allocation of resources to the gas-exchangeprocess. Key words: A/C_i curve, CO₂ assimilation, internal CO₂ partial pressure, photosynthesis     

一个新的家蚕转录相关锌带蛋白基因的克隆及序列分析

锌带蛋白(zinc ribbon protein )是锌指类蛋白的一种,它的Cys4 Zn(2+)结合位点由3个β₂片层折叠而成,而不是α螺旋结构。锌带结构与锌指结构同为转录因子结合核酸的结构域,锌带蛋白作为转录相关因子在调节基因表达活性等方面具有重要作用。在对家蚕 Bombyx mori蛹cDNA文库测序中,发现一个新的编码家蚕锌带蛋白基因的EST序列（GenBank 登录号DY230964）,以此序列为信息探针检索家蚕EST数据库,通过同源筛选,获得一个新的家蚕锌带蛋白基因cDNA全序列并经RT-PCR检测和克隆、测序验证,结果表明与电子克隆序列完全一致。我们将其命名为 BmZNRD1 (Zinc Ribbon Domain Containing 1)（GenBank登录号DQ432055）。该基因全长为675 bp,由363 bp的开放阅读框序列(ORF)、10 bp的5′端非翻译区序列(5′UTR)和302 bp 的3′端非编码区序列(3′ UTR)组成,其编码的120个氨基酸序列与其他真核生物间具有较高的同源性（达60%左右）,预测分子量为13.54 kD, 等电点为6.8。BmZNRD1编码的氨基酸序列是一种锌带蛋白,推测有2个功能结构域,分别是位于N-端的Cx₂Cx₁₄Cx₂C和C-端的Cx₂Cx₂₄Cx₂C,其中C-端保守氨基酸序列Cx₂Cx₆Yx₃QxRSADEx₂TxFx₂Cx₂C在生物进化中保守性很高,从酵母、果蝇、线虫到两栖类、哺乳类都有发现该结构域的存在,与酵母RNA聚合酶A亚单位9和转录相关蛋白有很高的相似性,推测其具有相同的功能。将BmZNRD1基因cDNA序列与家蚕基因组序列进行比对,结果表明该基因具有3个外显子,2个内含子,外显子/内含子边界符合经典的GT-AG规则。 关键词： 家蚕; 锌带蛋白基因; 电子克隆; 基因克隆; 序列分析     

The Effects of Temperature on Leaf Growth in Cyperus longus, a Temperate C4 Species

Plants of the C₄ sedge Cyperus longus L. were grown at 10, 20and 30 °C. An asymptotic growth curve, the Richards function,was fitted to growth data for successive leaves. The mean rateof leaf appearance was a linear function of temperature with0.014 leaves appearing per day for every 1 °C increase intemperature. The instantaneous relative rate of leaf extensionshowed a marked ontogenetic drift which was most rapid at 30°C and slowest at 10 °C. The mean absolute extensionrate for foliage had a temperature coefficient of 0.16 cm d^–1° C^–1 in the range from 10 to 30 °C. The durationof leaf growth was independent of leaf number at 10 and 20 °Cbut increased linearly with leaf number at 30 °C. The smalldifferences in relative growth rate at the three temperaturesresulted in large differences in foliage area produced at theend of a 30 d growth period. The final foliage areas at 20 and10 °C were 51 and 9% respectively of that at 30 °C. Cyperus longus, temperature, leaf growth, Richards function, growth analysis     

Homologous unequal cross-over within the human CYP2A gene cluster as a mechanism for the deletion of the entire CYP2A6 gene associated with the poor metabolizer phenotype.

To clarify the molecular mechanisms involved in the generation of the CYP2A6 gene deletion (E-type variant), we analyzed the CYP2A7 gene, which is located in the 5'-flanking region of the CYP2A6 gene, from individuals with the E-type variant and compared it with the sequences of wild type CYP2A7 and CYP2A6 genes. The 3'-downstream sequence (up to 324 bp from the SacI site in exon 9) of the CYP2A7 gene of the E-type variant is identical to that of the wild CYP2A7 gene. However, the 3'-downstream sequence (starting from 325 bp from the SacI site in exon 9) of the CYP2A7 gene of the E-type variant is identical to that of the wild CYP2A6 gene, indicating that the 3'-downstream region of CYP2A7 and the 3'-downstream region of CYP2A6 linked directly eliminating the whole CYP2A6 gene. PCR analysis using primers specific to the CYP2A7 gene and the CYP2A6 and CYP2A7 genes confirmed that all DNA samples obtained from 7 individuals carrying the E-type variant possessed the same break points. These results indicate that the breakpoint of the CYP2A6 gene deletion lies in the 3'-downstream region of the CYP2A7 and CYP2A6 genes.     

The Response of the C3-CAM Tree, Clusia rosea, to Light and Water Stress: I. GAS EXCHANGE CHARACTERISTICS

Gas exchange measurements were undertaken on 2-year-old plantsof Clusia rosea. The plants were shown to have the ability toswitch from C₃-photosynthesis to CAM and vice versa regardlessof leaf age and, under some conditions, CO₂ was taken up continuously,throughout the day and night. The light response was saturatedby 120 µmol m^–2 s^–1 typical of a shade plant. Gas exchange patterns in response to light, water and VPD wereexamined. All combinations of daytime and night-time CO₂ uptakewere observed, with rates of CO₂ uptake ranging from 2 to 11µmol m^–2 s^–1 depending upon water status andlight. Categorization of this plant asC₃, CAM or an intermediateis impossible. Differing VPD affected the magnitude of changesfrom CAM to C₃-photosynthesis (0 to 0.5 and 0 to 6.0 µmolm^–2 s^–1 CO₂, respectively) when plants were watered.Under well-watered conditions, but not under water stress, highPPFD elicited changes from CAM to C₃ gas exchange. This is unusualnot only for a shade plant but also for a plant with CAM. Itis of ecological importance for C. rosea, which may spend theearly years of its life as an epiphyte or in the forest understorey,to be able to maximize photosynthesis with minimal water loss. Key words: Clusia rosea, CAM, C₃, stress     

Partial Reduction in Activities of Photorespiratory Enzymes in C3-C4 Intermediates of Alternanthera and Parthenium

The maximum catalytic activities of several photorespiratoryand photosynthetic enzymes were determined in leaf extractsof three C₃–C₄ intermediates (Alternanthera ficoides,A. tenella and Parthenium hysterophorus) and were compared tothose of C₃ (A. sessiles, Pisum sativum) and C₄ (A. pungens,Zea mays and Amaranthus hypochondriacus) species. The activitylevels of key photorespiratory enzymes, glycolate oxidase, catalase,NADH-hydroxypyruvate reductase and glycerate kinase were less(28 to 35% reduced) in intermediates than those of typical C₃species. Similarly, the activities of photorespiratory aminotransferasesin the C₃–C₄ intermediates were also partially reduced(23 to 37% reduction). The activities of phosphoenolpyruvatecarboxylase (PEPC), pyruvate, orthophosphate dikinase and NAD-malicenzyme were higher (2 to 7 times) in leaf extracts of the intermediatesthan those of C₃ species. But the ratios of PEPC/rubisco inthe C₃–C₄ intermediates were more like C₃ than C₄ species.We draw attention to the partial reduction in enzyme activityof photorespiratory metabolism, which could be an importantfactor for restriction of photorespiration in the C₃–C₄intermediate species, in addition to enzyme compartmentationand/or operation of a ‘C₄-like’ cycle Key words: C₃–C₄ intermediates, C₄ pathway, enzyme profile, glycolate metabolism, photorespiration, photosynthesis     

Location of the 11 bp exon in the chicken pro alpha 2(I) collagen gene.

During the fine structural analysis of the 5' end of the 38 kb chicken pro alpha 2(I) collagen gene, we failed to locate an exon, only 11 bp in size, which had been predicted from the DNA sequence analysis of a cDNA clone complementary to the 5' end of the pro alpha 2(I) collagen mRNA (1). We know report the location of this 11 bp exon, exon 2, at the 5' end of a 180 bp Pst I fragment, 1900 bp 3' to exon 1 and 600 bp 5' to exon 3. Its sequence, ATGTGAGTGAG, is highly unusual in that it contains two overlapping consensus donor splice sequences. Moreover, it is flanked by two overlapping donor splice sequences but only one of the four splice sequences is actually spliced (1). The first half of intron 1 also has an unusual sequence: it is 68% GC, contains 88 CpG dinucleotides and 11 Hpa II sites. The second half is more like other intron sequences in the collagen gene with a GC content of 41%, 19 CpG, and no Hpa II sites. However it contains two sequences with 7 and 9 bp homology to the 14 bp SV40 enhancer core sequence. It is suggested that some part of intron 1 may be involved in regulation.     

The Responses of Net Photosysthesis to Light and Temperature in Spartina townsendii(sensu lato), a C4 Species from a Cool Temperate Climate

Carbon dioxide and water vapour exchanges for single attachedleaves of the temperate C₄ grass Spartina townsendii were measuredunder controlled environment conditions in an open gas-exchangesystem. The responses of net photosynthesis, stomatal resistance,and residual resistance to leaf temperature and photon fluxdensity are described. The light and temperature responses ofnet photosynthesis in S. townsendii are compared to informationon these responses in both temperate C₃ grasses and sub-tropicalC₄ grasses. Adaptation of photosynthesis in this C₄ speciesto a cool temperate climate is indicated both by the light andtemperature responses of net photo-synthesis. Unlike the C₄grasses examined previously, significant rates of net photosynthesiscan be detected at leaf temperatures below 10?C. Rates of netphotosynthesis equal or exceed those reported for temperateC₃ grasses at all of the temperature (5–40?C) and photonflax density (13–2500µmol m^–2 s^–1) conditionsexamined. Maximum rates of net photosynthesis in S. townsendiiare almost double those reported for C₃ herbage grasses. Unliketemperate C₃ grasses, the major limitation to net photosynthesisat low leaf temperatures (10?C and below) is the stomatal resistance,showing that the low residual resistance characteristic of C₄species is maintained in S. townsendii even at low leaf temperatures.     

Computational analysis of RNA editing sites in plant mitochondrial genomes reveals similar information content and a sporadic distribution of editing sites

A computational analysis of RNA editing sites was performedon protein-coding sequences of plant mitochondrial genomes fromArabidopsis thaliana, Beta vulgaris, Brassica napus, and Oryzasativa. The distribution of nucleotides around edited and uneditedcytidines was compared in 41 nucleotide segments and included1481 edited cytidines and 21,390 unedited cytidines in the 4genomes. The distribution of nucleotides was examined in 1,2, and 3 nucleotide windows by comparison of nucleotide frequencyratios and relative entropy. The relative entropy analyses indicatethat information is encoded in the nucleotide sequences in the5 prime flank (–18 to –14, –13 to –10,–6 to –4, –2/–1) and the immediate 3prime flanking nucleotide (+1), and these regions may be importantin editing site recognition. The relative entropy was largewhen 2 or 3 nucleotide windows were analyzed, suggesting thatseveral contiguous nucleotides may be involved in editing siterecognition. RNA editing sites were frequently preceded by 2pyrimidines or AU and followed by a guanidine (HYCG) in themonocot and dicot mitochondrial genomes, and rarely precededby 2 purines. Analysis of chloroplast editing sites from a dicot,Nicotiana tabacum, and a monocot, Zea mays, revealed a similardistribution of nucleotides around editing sites (HYCA). Thesimilarity of this motif around editing sites in monocots anddicots in both mitochondria and chloroplasts suggests that amechanistic basis for this motif exists that is common in thesedifferent organelle and phylogenetic systems. The preferredsequence distribution around RNA editing sites may have an importantimpact on the acquisition of editing sites in evolution becausethe immediate sequence context of a cytidine residue may rendera cytidine editable or uneditable, and consequently determinewhether a T to C mutation at a specific position may be correctedby RNA editing. The distribution of editing sites in many protein-codingsequences is shown to be non-random with editing sites clusteredin groups separated by regions with no editing sites. The sporadicdistribution of editing sites could result from a mechanismof editing site loss by gene conversion utilizing edited sequenceinformation, possibly through an edited cDNA intermediate.     

Effect of Low Relative Humidity on {delta}13C Value in Two C3 Grasses and in Panicum milioides, a C3-C4 Intermediate Species

When grown under conditions of low relative humidity, the C₃–C₄intermediate Panicum milioides, as well as the C₃ grasses Triticumaestivum and Poa pratense, exhibited ¹³C values which were upto 2–7%o less negative than the ¹³C values of the correspondingplants grown at high relative humidity. At both humidity levels,there was no evidence of a substantial contribution of phosphoenolpyruvatecarboxylase to carbon gain in Panicum milioides     

Seed Viability Constants for Lettuce

Seeds of two lettuce cultivars (Lactuca sativa L., cv. Meikoninginand cv. Grand Rapids) were hermetically stored with constantmoisture contents ranging between 3.6 and 17.9 per cent (freshweight basis) at constant temperatures ranging between 5 and75 °C. The decline with time in percentage germination andpercentage normal seedlings was determined for each storagetreatment. The data were fitted to an equation which containsthe constants: K₁, the probit of the initial percentage germinationor normal seedlings; K_E, a species constant; C_W, the constantof a logarithmic moisture term; C_H, the constant of a lineartemperature term and C_Q, the constant of a quadratic temperatureterm. Regression analysis of data from storage periods up to5.5 years at temperatures of 5–75 °C and seed moisturecontents of 3.6–13.6 per cent yielded the following values:K_E= 8.218, C_W=4.797±0.163, C_H=0.0489±0.0050 andC_Q=0.000365±0.000056. Although this equation consistentlyprovided a better fit, simplified equations, assuming eithera log-linear relationship between seed longevity and temperature,or a log-linear relationship between seed longevity and bothmoisture content and temperature, accounted for more than 94per cent of the variation at the restricted temperature rangeof 5–40 °C. Longevity of the same seed lots at sub-zero temperatures (–5,–10 and –20 °C) was studied in separate tests.Freezing damage, resulting in abnormal seedlings in the germinationtest, occurred at –20 °C when the moisture contentof the seeds exceeded 12 per cent. No decline in percentagenormal seedlings was observed after a storage period of 18 monthsor longer at –20 °C, provided the seed moisture contentdid not exceed 9.5 per cent. For seeds stored at –5 and–10 °C with 9.6–12.5 per cent moisture content,the observed rate of decline of percentage normal seedlingswas adequately predicted by the viability equation, using theabove values for the constants. This suggests that for low moisturecontents the viability equation can be applied to estimate longevityat sub-zero temperatures. Lettuce, Lactuca sativa (L.), seed longevity, seed storage, viability constants, storage conditions