Journal of Genetics and Genomics

Intracellular compartmentation of CTP synthase in Drosophila

Ji-Long Liu

2010, 37(5): 281-296. doi: 10.1016/S1673-8527(09)60046-1

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Abstract:
Compartmentation is essential for the localization of biological processes within a eukaryotic cell. ATP synthase localizes to organelles such as mitochondria and chloroplasts. By contrast, little is known about the subcellular distribution of CTP synthase, the critical enzyme in the production of CTP, a high-energy molecule similar to ATP. Here I describe the identification of a novel intracellular structure containing CTP synthase, termed the cytoophidium, inDrosophila cells. I find that cytoophidia are present in all major cell types in the ovary and exist in a wide range of tissues such as brain, gut, trachea, testis, accessory gland, salivary gland and lymph gland. In addition, I find CTP synthase-containing cytoophidia in other fruit fly species. The observation of compartmentation of CTP synthase now permits a broad range of questions to be addressed concerning not only the structure and function of cytoophidia but also the organization and regulation of CTP synthesis.

Methylation patterns in 5′ terminal regions of pluripotency-related genes in bovine in vitro fertilized and cloned embryos

Jie Lan, Song Hua, Hailin Zhang, Yongli Song, Jun Liu, Yong Zhang

2010, 37(5): 297-304. doi: 10.1016/S1673-8527(09)60047-3

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Abstract:
In order to investigate DNA methylation profiles of five pluripotency-related genes (Oct4, Sox2, Nanog, Rex1 and Fgf4) during bovine maternal to zygotic transition (MZT) in both in vitro fertilized (IVF) and nuclear transfer (NT) embryos, sodium bisulfite sequencing method was used to detect DNA methylation levels, accompanied by the statistical analysis of embryo developmental rates. The results showed that Oct4, Nanog, Rex1 and Fgf4 were respectively demethylated by 25.22% (P < 0.01), 3.84% ( P > 0.05), 31.82% ( P < 0.01) and 10% ( P > 0.05) while Sox2 retained unmethylation during MZT in IVF embryos. By contrast, Oct4 and Rex1 respectively underwent demethylation by 23.04% (P < 0.01) and 6.02% ( P > 0.05), and, reversely, Sox2, Nanog and Fgf4 respectively experienced remethylation by 0.84% (P > 0.05), 5.39% ( P > 0.05) and 5.46% ( P > 0.05) during MZT in NT embryos. Interestingly, the CpG 14 site of Sox2 was specifically methylated in both 8-cell and morula NT embryos. In addition, the development of blastocysts between IVF and NT embryos showed no significant difference. DNA methylation analysis showed that only Oct4 and Sox2 underwent the correct methylation reprogramming process, which may be responsible for the development of blastocysts of NT embryos to a certain extent. In conclusion, the five genes respectively experienced demethylation to different extents and incomplete DNA methylation reprogramming during bovine MZT in both IVF and NT embryos, suggesting that they may be used as indicators for bovine embryo developmental competence.

Natural selection maintains the transcribed LTR retrotransposons in Nosema bombycis

Heng Xiang, Guoqing Pan, Ruizhi Zhang, Jinshan Xu, Tian Li, Wenle Li, Zeyang Zhou, Zhonghuai Xiang

2010, 37(5): 305-314. doi: 10.1016/S1673-8527(09)60048-5

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Abstract:
Eight intact LTR retrotransposons (Nbr1–Nbr8) have been previously characterized from the genome of Nosema bombycis, a eukaryotic parasite with a compact and reduced genome. Here we describe six novel transcribed Nbr elements (Nbr9–Nbr14) identified through either cDNA library or RT-PCR. Like previously determined ones, all of them belong to the Ty3/Gypsy superfamily. Retrotransposon diversity and incomplete domains with insertions (Nbr12), deletions (Nbr11) and in-frame stop codons in coding regions (Nbr9) were detected, suggesting that both defective and loss events of LTR retrotransposon have happened in N. bombycis genome. Analysis of selection showed that strong purifying selection acts on all elements except Nbr11. This implies that selective pressure keeps both these Nbrs and their functions in genome. Interestingly, Nbr11 is under positive selection and some positively selected codons were identified, indicating that new functionality might have evolved in the Nbr11 retrotransposon. Unlike other transposable elements, Nbr11 has integrated into a conserved syntenic block and probably resulted in the inversion of both flanking regions. This demonstrates that transposable element is an important factor for the reshuffling and evolution of their host genomes, and may be maintained under natural selection.

The phylogeny of Orthoptera inferred from mtDNA and description of Elimaea cheni (Tettigoniidae: Phaneropterinae) mitogenome

Zhijun Zhou, Haiyan Ye, Yuan Huang, Fuming Shi

2010, 37(5): 315-324. doi: 10.1016/S1673-8527(09)60049-7

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Abstract:
The complete 15,831 bp nucleotide sequence of the mitochondrial genome from Elimaea cheni (Phaneropterinae) was determined. The putative initiation codon for cox1 was TTA. The phylogeny of Orthoptera based on different mtDNA datasets were analyzed with maximum likelihood (ML) and Bayesian inference (BI). When all 37 genes (mtDNA) were analyzed simultaneously, the monophyly of Caelifera and Ensifera were recovered in the context of our taxon sampling. The phylogeny of Orthoptera was largely consistent with previous phylogenetic hypotheses. Rhaphidophoridae to be a sister group of Tettigoniidae, and the relationships among four subfamilies of Tettigoniidae were (Phaneropterinae + (Conocephalinae + (Bradyporinae + Tettigoniinae))). Pyrgomorphidae was the most basal group of Caelifera. The relationships among six acridid subfamilies were (Oedipodinae + (Acridinae + (Gomphocerinae + (Oxyinae + (Calliptaminae + Cyrtacanthacridinae))))). However, we did not recover a monophyletic Grylloidea. Myrmecophilidae clustered into one clade with Gryllotalpidae instead of with Gryllidae. ML and BI analyses of all protein coding genes (using all nucleotide sequence data or excluding the third codon position, and amino acid sequences) revealed a topology identical to that of the entire mtDNA genome dataset. However, 22 tRNAs genes excluding the DHU loop and TψC loop (TRNA), and two rRNA genes (RRNA) perform poorly when analyzed as single dataset. Our results suggest that the best phylogenetic inferences were ML and BI methods based on total mtDNA. Excluding tRNA genes, rRNA genes and the third codon position of protein coding genes from dataset and converting nucleotide sequences to amino acid sequences do not positively affect phylogenetic reconstruction.

Genetic analysis of leaffolder resistance in rice

Yuchun Rao, Guojun Dong, Dali Zeng, Jiang Hu, Longjun Zeng, Zhengyu Gao, Guanghen Zhang, Longbiao Guo, Qian Qian

2010, 37(5): 325-331. doi: 10.1016/S1673-8527(09)60050-3

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Abstract:
A double haploid (DH) population, which consists of 120 lines derived from anther culture of a typical indica and japonica hybrid ‘CJ06’/‘TN1’, was used to investigate the genetic basis for rice leaffolder resistance. Using a constructed molecular linkage map, five QTLs for rolled leaves were detected on chromosomes 1, 2, 3, 4, and 8. The positive alleles from CJ06 on chromosomes 3, 4, and 8 increased the resistance to rice leaffolder, and the alleles from TN1 on chromosomes 1 and 2 also enhanced resistance to leaffolder. The interactions between QTLs were identified and tested, and four conditional interactions were acquired for resistance to rice leaffolder. These loci were located on chromosomes 2, 9, 10, and 11, respectively. QTL pyramiding indicated that the positive alleles affect resistance to leaffolder. The prospective application of this data in rice breeding was also discussed.

Characterization of seedling proteomes and development of markers to distinguish the Brassica A and C genomes

Fang Kong, Cailin Ge, Xiaoping Fang, Rod J. Snowdon, Youping Wang

2010, 37(5): 333-340. doi: 10.1016/S1673-8527(09)60051-5

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Abstract:
The diploid species Brassica rapa (genome AA) and B. oleracea (genome CC) were compared by full-scale proteome analyses of seedling. A total of 28.2% of the proteins was common to both species, indicating the existence of a basal or ubiquitous proteome. However, a number of discriminating proteins (32.0%) and specific proteins (39.8%) of the Brassica A and C genomes, respectively, were identified, which could represent potentially species-specific functions. Based on these A or C genome-specific proteins, a number of PCR-based markers to distinguish B. rapa and B. oleracea species were also developed.

Feasible and reliable quantification of mRNA in Arabidopsis thaliana using optical thin-film biosensor chips

Sulan Bai, Fan Wang, Zhen Zhang, Shucheng Li, Jie Zhang, Yaochuan Zhang

2010, 37(5): 341-346. doi: 10.1016/S1673-8527(09)60052-7

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Abstract:
mRNA quantification is very important in molecular biological researches. Traditional spectrophotometric method cannot distinguish DNA, rRNA and tRNA species from mRNA. Northern blot can be used for mRNA quantification but is known to be time consuming. To rapidly detect mRNA levels, we developed an optical thin-film biosensor chip based method, to quantify mRNA in samples. After total RNA was extracted, the mRNA with poly(A) tails was reverse transcribed with oligo(dT)₂₀ primers and dNTPs mixed with digoxigenin(DIG)-11-dUTP. The transcribed first strand cDNA was hybridized with oligo(dA)₂₀ nucleotide probes spotted on optical thin-film biosensor chips. Excess first strand cDNA, single-strand RNA, and mis-matched DNA/DNA hybrids were removed by washing. The perfect-matched DNA/DNA hybrid was detected with anti-DIG-AP (alkaline phosphatase) conjugate and then incubated with NBT/BCIP substrate for color development. The range of the color is from purplish red to blue, according to the cDNA mass deposited on chip surface. Detection of mRNA levels from Arabidopsis samples proved that this method is feasible for mRNA quantification, and has great potential for application in mRNA quantification in various organisms.

2010 Vol. 37, No. 5