Vitamin C transporter gene (SLC23A1 and SLC23A2) polymorphisms, plasma vitamin C levels, and gastric cancer risk in the EPIC cohort

Vitamin C is known to protect mucosal tissues from oxidative stress and inhibit nitrosamine formation in the stomach. High consumption of fruits, particularly citrus, and higher circulating vitamin C concentrations may be inversely associated with gastric cancer (GC) risk. We investigated 20 polymorphisms in vitamin C transporter genes SCL23A1 and SCL23A2 and GC risk in 365 cases and 1,284 controls nested within the European Prospective Investigation into Cancer and Nutrition cohort. We also evaluated the association between these polymorphisms and baseline plasma vitamin C levels in a subset of participants. Four SNPs were predictors of plasma vitamin C levels (SLC23A1 rs11950646 and rs33972313; SLC23A2 rs6053005 and rs6133175) in multivariable linear regression models. One SNP (SLC23A2 rs6116569) was associated with GC risk, in particular non-cardia GC (OR = 1.63, 95 % CI = 1.11–2.39, based on 178 non-cardia cases), but this association was attenuated when plasma vitamin C was included in the logistic regression model. Haplotype analysis of SLC23A1 yielded no associations with GC. In SLC23A2, one haplotype was associated with both overall and non-cardia GC, another haplotype was associated with GC overall, and a third was associated with intestinal-type GC. Common variants in SLC23A1 and SLC23A2 may influence plasma vitamin C concentration independent of dietary intake, and variation in SLC23A2 may influence GC risk. Additional prospective studies in large populations and consortia are recommended. Investigation of variation in vitamin C transporter genes may shed light on the preventative properties of vitamin C in gastric carcinogenesis.     

Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis

Warm-blooded vertebrates show large-scale variation in G + C content along their chromosomes, a pattern which appears to be largely absent from cold-blooded vertebrates. However, compositional variation in poikilotherms has generally been studied by ultracentrifugation rather than sequence analysis. In this paper, we investigate the compositional properties of coding sequences from a broad range of vertebrate poikilotherms using DNA sequence analysis. We find that on average poikilotherms have lower third-codon position GC contents (GC3) than homeotherms but that some poikilotherms have higher mean GC3 values. We find that most poikilotherms have lower variation in GC3 than homeotherms but that there is a correlation between GC12 and GC3 for some species, indicating that there is systematic variation in base composition across their genomes. We also demonstrate that the GC3 of genes in the zebrafish, Danio rerio, is correlated with that in humans, suggesting that vertebrates share a basic isochore structure. However, we find no correlation between either the mean GC3 or the standard deviation in GC3 and body temperature.     

Induction of alpha-caveolin-1 (alphaCAV1) expression in bovine granulosa cells in response to an ovulatory dose of human chorionic gonadotropin

Caveolins are implicated in endocytosis, cholesterol trafficking and signal transduction. A cDNA fragment corresponding to caveolin-1 (CAV1) was identified in a mRNA profiling expression study in bovine granulosa cells (GC) following human chorionic gonadotropin (hCG)-induced ovulation. Thus, we have characterized CAV1 cDNA and studied its spatio-temporal expression pattern in bovine ovarian follicles. The full-length bovine alphaCAV1 cDNA was cloned and encodes a putative 22 kDa protein. Expression of alphaCAV1 was studied in bovine GC obtained from follicles at different developmental stages: small follicles (SF: 2-4 mm), dominant follicles (DF), ovulatory follicles (OF: 24 hr post-hCG), and corpus luteum (CL). Semiquantitative RT-PCR analysis showed a 6.5-fold increase in alphaCAV1 mRNA in GC of OF versus DF (P < 0.0001), whereas CAV2 mRNA was increased by only twofold (P < 0.0007). Temporal expression of alphaCAV1 mRNA from OF recovered at 0, 6, 12, 18, and 24 hr after hCG injection showed an 8.5-fold increase of alphaCAV1 mRNA after 24 hr compared to 0 hr (P < 0.0018) whereas no significant variation was detected for CAV2. Immunoblot demonstrated an initial increase in alphaCAV1 protein level 12 hr post-hCG, reaching a maximum at 24 hr. Immunohistochemical localization of CAV1 was observed in GC of OF isolated 18 and 24 hr after hCG injection, whereas no signal was detected in GC of DF and SF. The induction of alphaCAV1 in GC of OF suggests that alphaCAV1 likely contributes to control the increase in membrane signaling that occurs at the time of ovulation and luteinization.     

Reinvestigation on the causes of genomic GC variation between the orthologous genes of Mycobacterium tuberculosis and Mycobacterium leprae

Genomic GC (overall G+C content of the coding sequences) variations were reinvestigated between the orthologous genes of Mycobacterium tuberculosis and Mycobacterium leprae species. It was observed that overall genomic GC variation between the species mainly originates from the combined effects GC(1) and GC(2) variations. But codons having identical amino acids with different codons (IA) (between the orthologous codon pairs) are responsible for the genomic GC(3) variation between the organisms, whereas orthologous codons having different amino acids (DA) between the two organisms are responsible for the variation of GC(1) levels. Further analyses indicate that duets and quartets are going in the same direction with same magnitude in changing the GC(3) levels for IA category, whereas GC(1) levels of duets of DA category decreases significantly from the overall GC(1) levels but GC(1) levels of quartets increases significantly from the overall GC(1) levels. GC(3) levels of informational genes for the IA category decrease more rapidly than the other functional categories of genes. The biological implications of these results have been discussed in this paper.     

Evidence that Natural Selection is the Primary Cause of the Guanine-cytosine Content Variation in Rice Genes

Cereal genes are classified into two distinct classes according to the guanine-cytosine （GC） content at the third codon sites （GC3）. Natural selection and mutation bias have been proposed to affect the GC content. However, there has been controversy about the cause of GC variation. Here, we characterized the GC content of 1 092 paralogs and other single-copy genes in the duplicated chromosomal regions of the rice genome （ssp. indica） and classified the paralogs into GC3-rich and GC3-poor groups. By referring to out-group sequences from Arabidopsis and maize, we confirmed that the average synonymous substitution rate of the GC3-rich genes is significantly lower than that of the GC3-poor genes. Furthermore, we explored the other possible factors corresponding to the GC variation including the length of coding sequences, the number of exons in each gene, the number of genes in each family, the location of genes on chromosomes and the protein functions. Consequently, we propose that natural selection rather than mutation bias was the primary cause of the GC variation.     

Multiple Divergent ITS1 Copies Were Identified in Single Tomato Genome Using DGGE Analysis

The intra-genomic variation in the internal transcribed spacer (ITS) region has led to misleading conclusions in the evolutionary analysis of plants; understanding this variation is critical for correct evolutionary analysis based on ITS sequences. To reveal the ITS variation in tomato, entire copies of ITS1 sequences within tomato species were separated using denaturing gradient gel electrophoresis (DGGE) and DNA sequence analysis. ITS1 copies varied significantly in sequence composition, but not in sequence length within the same tomato cultivar. DNA sequence similarity of the ITS1 copies was 77–100 %. Moreover, AT and GC contents in ITS1 copies from each tomato cultivar were significantly different, ranging from 50.4 to 64.3 % for GC and from 35.7 to 49.6 % for AT. However, the length variation of ITS1 was insignificant, ranging from 279 to 282 bp. Multiple copies of divergent ITS1 present in the tomato genome indicate that some copies may be paralogues. In conclusion, DGGE technique is a reliable and novel approach to reveal the entire ITS copy variation and the possible evolutionary relationship of tomato.     

On the molecular mechanism of GC content variation among eubacterial genomes

Background  

As a key parameter of genome sequence variation, the GC content of bacterial genomes has been investigated for over half a century, and many hypotheses have been put forward to explain this GC content variation and its relationship to other fundamental processes. Previously, we classified eubacteria into dnaE-based groups (the dimeric combination of DNA polymerase III alpha subunits), according to a hypothesis where GC content variation is essentially governed by genome replication and DNA repair mechanisms. Further investigation led to the discovery that two major mutator genes, polC and dnaE2, may be responsible for genomic GC content variation. Consequently, an in-depth analysis was conducted to evaluate various potential intrinsic and extrinsic factors in association with GC content variation among eubacterial genomes.     

A thermal denaturation study of the genomic DNAs from the North American genera of the fish family Percidae

The genomic DNAs of 1 1 species of percid fishes representing the five recognized North American genera are characterized using data from thermal denaturation assays. Base compositions were estimated from the transitional melting temperature of native and sonicated DNA and expressed as per cent guanine-cytosine (%GC) values. Among genera, %GC values for native DNAs (c, 23,000 base pairs in length) range between 38.3% GC for yellow perch, Perca flavescens (Mitchill), to 43.2% GC for sauger, Stizostedion cunadense (Smith). Significant variation in %GC values was observed among surveyed genera of the subfamily Percinae, which include Perca, Percinu, Etheostoma and Ammocrypfa . Melting profiles were generated for each species, and distinct GC rich regions were identified within the genomes of walleye, Sfizostcdion virreum (Mitchill) and Etheostoma spp. Compositional heterogeneity (CH) and asymmetry values were calculated from melting profile data. Patterns of variation in genomic characters differed among the genera surveyed. Members of the speciose genus Etheostomu showed relatively little variation in genomic characters, whereas Stizosredion exhibited significant interspecific variation.     

Evolution of genome size across some cultivated Allium species.

Allium L. (Alliaceae), a genus of major economic importance, exhibits a great diversity in various morphological characters and particularly in life form, with bulbs and rhizomes. Allium species show variation in several cytogenetic characters such as basic chromosome number, ploidy level, and genome size. The purpose of the present investigation was to study the evolution of nuclear DNA amount, GC content, and life form. A phylogenetic approach was used on a sample of 30 Allium species, including major vegetable crops and their wild allies, belonging to the 3 major subgenera Allium, Amerallium, and Rhizirideum and 14 sections. A phylogeny was constructed using internal transcribed spacer (ITS) sequences of 43 accessions representing 30 species, and the nuclear DNA amount and the GC content of 24 Allium species were investigated by flow cytometry. For the first time, the nuclear DNA content of Allium cyaneum and Allium vavilovii was measured, and the GC content of 16 species was measured. We addressed the following questions: (i) Is the variation in nuclear DNA amount and GC content linked to the evolutionary history of these edible Allium species and their wild relatives? (ii) How did life form (rhizome or bulb) evolve in edible Allium? Our results revealed significant interspecific variation in the nuclear DNA amount as well as in the GC content. No correlation was found between the GC content and the nuclear DNA amount. The reconstruction of nuclear DNA amount on the phylogeny showed a tendency towards a decrease in genome size within the genus. The reconstruction of life form history showed that rhizomes evolved in the subgenus Rhizirideum from an ancestral bulbous life form and were subsequently lost at least twice independently in this subgenus.     

Estrous cycle-regulated expression of CYP1B1 mRNA in the rat ovary

CYP1B1, a member of the cytochrome p450 superfamily, is expressed constitutively in the steroidogenic tissues of mammals and is inducible by peptide hormones, cAMP and aromatic hydrocarbon receptor (AHR) ligands. The mechanism of induction of this cytochrome p450 is similar to that for CYP1A1, i.e. through the aromatic hydrocarbon receptor (AHR) signaling pathway. We have recently reported that CYP1B1, but not CYP1A1, is expressed in rat granulosa cells (GC) in the absence of any external stimulus. The induction of CYP1B1 mRNA in rat GC by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in vitro was followed by an increase in AHR and estrogen receptor (ER-beta) RNA levels. Estrous cycle-dependent expression of AHR, AHR-nuclear translocator (ARNT) and ER-mRNAs in the rat ovary was reported. We suggest that CYP1B1 may play a major role in the regulation of rat ovarian function/cycle but until now this has been unexplored experimentally. The present study was therefore aimed at examining the expression of CYP1A1, CYP1B1 and ER-mRNA in rat ovarian tissues throughout the estrous cycle to establish any correlation in the expressions of these mRNAs in rat ovary. Total RNA was extracted from the ovary and liver of cycling adult rats and the mRNAs were analyzed using relative RT-PCR with gene-specific primers for the target mRNA and for RPL 19 or S16 primers as an internal control. The results indicated that in the ovary, CYP1B1 mRNA increased significantly on the evening of proestrus and dramatically decreased on the morning of estrus, while ER-mRNA remained unaltered throughout the estrous cycle. CYP1A1 mRNA in the ovary and both CYP1A1 and CYP1B1 mRNAs in the liver were undetectable. That the sudden decrease of ovarian CYP1B1 mRNA on the morning of estrus was not an effect of the LH surge was verified in vitro using our short-term GC culture model. GC prepared from rats super-stimulated with equine chorionic gonadotropin (eCG) were cultured for 6 h with or without LH and TCDD. It was observed that both CYP1A1 and CYP1B1 mRNAs were induced by TCDD with no apparent effect of LH. It is suggested that the high level of CYP1B1 mRNA expression on the evening of proestrus in rat ovary might be involved in metabolism of estrogens to catecholestrogen (a known effect of CYP1B1), and that expression is unaffected in GC by LH.     

Mapping of Genes for Cooking and Eating Qualities in Thai Jasmine Rice (KDML105)

Thai jasmine rice, KDML 105, is known as the best quality rice.It is known not only for its aroma but also for its good cookingand eating qualities. Amylose content (AC), gel consistency(GC) and gelatinization temperature (GT) are important traitsdetermining rice quality. A population of recombinant inbredlines (RIL) derived from KDML105 x CT9993 cross was used tostudy the genetic control of AC, GC and GT traits. A total of191 markers were used in the linkage map construction. The 1605.3cM linkage map covering nearly the whole rice genome was usedfor QTL (define QTL) analysis. Four QTLs for AC were detectedon chromosomes 3, 4, 6 and 7. These QTLs accounted for 80% ofphenotypic variation explained (PVE) in AC. The presence ofone major gene as well as several modifiers was responsiblefor the expression of the trait. Two QTLs on chromosome 6 andone on chromosome 7 were detected for GC, which accounts for57% of PVE. A single gene of major effect along with modifiergenes controls GC from this cross. The QTLs in the vicinityof waxy locus were major contributors in the expression of ACand GC. The finding that the position of QTLs for AC and GCwere near each other may reflect tight linkage or pleiotropy.Three QTLs were detected, one on chromosome 2 and two on chromosome6, which accounted for 67% of PVE in GT. Just like AC and GC,one major gene and modifier genes governed the variation inGT resulting from the KDML105 x CT9993 cross. Breeding for cookingand eating qualities will largely rely on the preferences ofthe end users.     

Synonymous codon usage in Thermosynechococcus elongatus (cyanobacteria) identifies the factors shaping codon usage variation

Analysis of synonymous codon usage pattern in the genome of a thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 using multivariate statistical analysis revealed a single major explanatory axis accounting for codon usage variation in the organism. This axis is correlated with the GC content at third base of synonymous codons (GC3s) in correspondence analysis taking T. elongatus genes. A negative correlation was observed between effective number of codons i.e. Nc and GC3s. Results suggested a mutational bias as the major factor in shaping codon usage in this cyanobacterium. In comparison to the lowly expressed genes, highly expressed genes of this organism possess significantly higher proportion of pyrimidine-ending codons suggesting that besides, mutational bias, translational selection also influenced codon usage variation in T. elongatus. Correspondence analysis of relative synonymous codon usage (RSCU) with A, T, G, C at third positions (A3s, T3s, G3s, C3s, respectively) also supported this fact and expression levels of genes and gene length also influenced codon usage. A role of translational accuracy was identified in dictating the codon usage variation of this genome. Results indicated that although mutational bias is the major factor in shaping codon usage in T. elongatus, factors like translational selection, translational accuracy and gene expression level also influenced codon usage variation.     

A Simple Model for the Influence of Meiotic Conversion Tracts on GC Content

A strong correlation between GC content and recombination rate is observed in many eukaryotes, which is thought to be due to conversion events linked to the repair of meiotic double-strand breaks. In several organisms, the length of conversion tracts has been shown to decrease exponentially with increasing distance from the sites of meiotic double-strand breaks. I show here that this behavior leads to a simple analytical model for the evolution and the equilibrium state of the GC content of sequences devoid of meiotic double-strand break sites. In the yeast Saccharomyces cerevisiae, meiotic double-strand breaks are practically excluded from protein-coding sequences. A good fit was observed between the predictions of the model and the variations of the average GC content of the third codon position (GC3) of S. cerevisiae genes. Moreover, recombination parameters that can be extracted by fitting the data to the model coincide with experimentally determined values. These results thus indicate that meiotic recombination plays an important part in determining the fluctuations of GC content in yeast coding sequences. The model also accounted for the different patterns of GC variations observed in the genes of Candida species that exhibit a variety of sexual lifestyles, and hence a wide range of meiotic recombination rates. Finally, the variations of the average GC3 content of human and chicken coding sequences could also be fitted by the model. These results suggest the existence of a widespread pattern of GC variation in eukaryotic genes due to meiotic recombination, which would imply the generality of two features of meiotic recombination: its association with GC-biased gene conversion and the quasi-exclusion of meiotic double-strand breaks from coding sequences. Moreover, the model points out to specific constraints on protein fragments encoded by exon terminal sequences, which are the most affected by the GC bias.     

Evidence that Natural Selection is the Primary Cause of the Guanine-cytosine Content Variation in Rice Genes

Cereal genes are classified into two distinct classes according to the guanine-cytosine(GC)content at the third codonsites(GC_3).Natural selection and mutation bias have been proposed to affect the GC content.However,there has beencontroversy about the cause of GC variation.Here,we characterized the GC content of 1092 paralogs and other single-copygenes in the duplicated chromosomal regions of the rice genome(ssp.indica)and classified the paralogs into GC_3-richand GC_3-poor groups.By referring to out-group sequences from Arabidopsis and maize,we confirmed that the averagesynonymous substitution rate of the GC_3-rich genes is significantly lower than that of the GC_3-poor genes.Furthermore,we explored the other possible factors corresponding to the GC variation including the length of coding sequences,thenumber of exons in each gene,the number of genes in each family,the location of genes on chromosomes and the proteinfunctions.Consequently,we propose that natural selection rather than mutation bias was the primary cause of the GCvariation.     

Codon usage in the G+C-rich Streptomyces genome.

The codon usage (CU) patterns of 64 genes from the Gram+ prokaryotic genus Streptomyces were analysed. Despite the extremely high overall G+C content of the Streptomyces genome (estimated at 0.74), individual genes varied in G+C content from 0.610 to 0.797, and had third codon position G+C contents (GC3s) that varied from 0.764 to 0.983. The variation in GC3s explains a significant proportion of the variation in CU patterns. This is consistent with an evolutionary model of the Streptomyces genome where biased mutation pressure has led to a high average G+C content with random variation about the mean, although the variation observed is greater than that expected from a simple binomial model. The only gene in the sample that can be confidently predicted to be highly expressed, EF-Tu of Streptomyces coelicolor A3(2) (GC3s = 0.927), shows a preference for a third position C in several of the four codon families, and for CGY and GGY for Arg and Gly codons, respectively (Y = pyrimidine); similar CU patterns are found in highly expressed genes of the G+C-rich Micrococcus luteus genome. It thus appears that codon usage in Streptomyces is determined predominantly by mutation bias, with weak translational selection operating only in highly expressed genes. We discuss the possible consequences of the extreme codon bias of Streptomyces and consider how it may have evolved. A set of CU tables is provided for use with computer programs that locate protein-coding regions.     

氨基酸转运载体SLC1A5在胃癌组织中的表达及其临床病理学意义

目的:研究氨基酸转运载体溶质载体家族1成员5(Solute Carrier Family 1 Member 5, SLC1A5)蛋白在胃癌组织中的表达情况,并探讨其与胃癌临床病理特征及预后的相关性。方法:收集进展期胃癌组织及对应癌旁组织90例,应用免疫组化技术检测SLC1A5在上述组织中的表达情况,并统计分析其表达与胃癌临床病理特征及预后的关系。同时通过基因数据库分析SLC1A5在胃癌组织和癌旁组织中表达情况及其对胃癌患者预后的影响。结果:与癌旁组织相比,胃癌组织中SLC1A5表达明显上调(P0.0001)。数据库研究也显示SLC1A5在胃癌组织中表达明显上调(GSE 65801,P=0.0046;GSE 63809,P0.0001;GSE 27342,P=0.0147)。胃癌组织中SLC1A5高表达与肿瘤大小(P0.05)、肿瘤浸润深度(P0.01)、淋巴结转移(P0.05)、TNM分期(P0.05)和Ki-67(P0.01)相关,而与年龄、性别、肿瘤位置及分化程度均无显著相关性(P0.05)。胃癌组织中SLC1A5表达强度与患者预后相关,表达越高,患者预后越差(总体生存率,P=0.0131;无复发生存率,P=0.0293)。数据库分析也显示SLC1A5高表达可明显缩短患者的总体生存期(GSE 14210,P=0.011;GSE 22377,P=0.0015)和无进展生存期(GSE 14210,P=0.0095;GSE 22377,P=0.0012)。结论:SLC1A5蛋白表达在胃癌组织中明显上调,且与肿瘤大小、肿瘤浸润深度、淋巴结转移及TNM分期有关。SLC1A5高表达与胃癌患者预后不良密切相关。     

Long noncoding RNA VCAN-AS1 contributes to the progression of gastric cancer via regulating p53 expression

Gastric cancer (GC) is one of the most frequent malignancies worldwide. Long noncoding RNAs (lncRNAs) are found to be largely implicated in various cancers, including GC. However, the function of lncRNA VCAN antisense RNA 1 (VCAN-AS1) in GC remains unclear. Herein, we observed a low level of VCAN-AS1 in normal gastric tissues through NCBI and UCSC, and that VCAN-AS1 upregulation in GC tissues was related to poor prognosis by TCGA. Furthermore, VCAN-AS1 was found markedly enhanced in GC tissues and cell lines, while its upregulation was related with clinical outcomes of GC patients. Besides this, silencing VCAN-AS1 represses cell proliferation, migration, and invasion but enhances apoptosis. More important, we discovered that VCAN-AS1 expression was negatively correlated with wild-type p53 levels in GC tissues and that p53 was negatively modulated by VCAN-AS1 in GC cells. Furthermore, p53 suppression reversed the repression of VCAN-AS1 silence on the biological processes of AGS cells. Intriguingly, we identified that both VCAN-AS1 and TP53 can bind with eIF4A3, one of the core proteins in the exon junction complex. Also, we confirmed that VCAN-AS1 negatively regulates TP53 expression by competitively binding with eIF4A3. Our findings disclosed that VCAN-AS1 contributes to GC progression through interacting with eIF4A3 to downregulate TP53 expression, indicating that VCAN-AS1 is a novel therapeutic strategy for GC treatment.     

普通野生稻线粒体蛋白质编码基因密码子使用偏好性的分析

以普通野生稻(Oryza rufipogon Griff.)线粒体基因组为对象,分析其蛋白质编码基因的密码子使用特征及与亚洲栽培稻(O. sativa L.)的差异,探讨其密码子偏性形成的影响因素和进化过程。结果显示:普通野生稻线粒体基因组编码序列第1、第2和第3位碱基的GC含量依次为49.18%、42.67%和40.86%;有效密码子数(Nc)分布于45.32～61.00之间,其密码子偏性较弱; Nc值仅与GC_3呈显著相关,密码子第3位的碱基组成对密码子偏性影响较大;第1向量轴上显示9.91%的差异,其与GC_3s、Nc、密码子偏好指数(CBI)和最优密码子使用频率(Fop)的相关性均达到显著水平;而GC_3和GC₁₂的相关性未达到显著水平。因此,普通野生稻线粒体基因组密码子的使用偏性主要受自然选择压力影响而形成。本研究确定了21个普通野生稻线粒体基因组的最优密码子,大多以A或T结尾,与叶绿体密码子具有趋同进化,但是与核基因组具有不同的偏好性。同义密码子相对使用度(RSCU)、PR2偏倚分析和中性绘图分析显示,普通野生稻线粒体基因功能和其密码子使用密切相关,且线粒体密码子使用在普通野生稻、粳稻(O. sativa L. subsp. japonica Kato)和籼稻(O. sativa L. subsp.indica Kato)内具有同质性。