Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns.
Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns.
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DOI：
10.1186/1471-2164-9-587
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发表时间：
2008-12-05
期刊：
影响因子：
4.4
通讯作者：
Huynen, Martijn A.
中科院分区：
文献类型：
--
作者：
Ricard, Guenola;de Graaf, Rob M.;Dutilh, Bas E.;Duarte, I.;van Alen, Theo A.;van Hoek, Angela H. A. M.;Boxma, Brigitte;van der Staay, Georg W. M.;Moon-van der Staay, Seung Yeo;Chang, Wei-Jen;Landweber, Laura F.;Hackstein, Johannes H. P.;Huynen, Martijn A.
卵圆夜兽是一种单细胞真核生物，具有产氢线粒体，生活在蟑螂的后肠中。像所有的纤毛虫分类单元的成员，它有两种类型的细胞核，一个微核和一个大核。n.卵圆藻通过形成多线染色体产生其大核染色体，所述多线染色体随后通过DNA消除和重排发育成大核染色体。我们研究了N.椭圆形。我们通过对大核DNA序列（4，242）和cDNA（5，484）进行测序并相互比较，确定了端粒、亚端粒区、UTR、编码区和内含子。端粒由重复序列CCC（AAAACCCC）n组成，类似于游仆虫、Sterkiella（Oxytricha）和柱甲等旋毛纤毛虫的端粒。每个测序的染色体，我们发现一个单一的蛋白质编码基因，一个单一的tRNA，或完整的核糖体RNA簇的证据。因此，染色体似乎编码单个转录本。在短的亚端粒区域，我们发现了一些过度表达的基序，可能参与基因调控，但没有共识的多聚腺苷酸化位点。内含子很短（21 - 29个核苷酸），并且很大一部分（1/3）的微小内含子在远缘纤毛动物草履虫中是保守的。如在P.tetraurelia中观察到的，N.卵形内含子倾向于包含框内终止密码子或具有不能被3整除的长度。在内含子保留的情况下，这种模式导致mRNA翻译的过早终止，并可能通过无义介导的mRNA衰变途径降解未剪接的mRNA。短的前导序列、微小的内含子和单个基因的组合导致非常小的大核染色体。我们发现的最小的只有150个核苷酸。
Nyctotherus ovalis is a single-celled eukaryote that has hydrogen-producing mitochondria and lives in the hindgut of cockroaches. Like all members of the ciliate taxon, it has two types of nuclei, a micronucleus and a macronucleus. N. ovalis generates its macronuclear chromosomes by forming polytene chromosomes that subsequently develop into macronuclear chromosomes by DNA elimination and rearrangement. We examined the structure of these gene-sized macronuclear chromosomes in N. ovalis. We determined the telomeres, subtelomeric regions, UTRs, coding regions and introns by sequencing a large set of macronuclear DNA sequences (4,242) and cDNAs (5,484) and comparing them with each other. The telomeres consist of repeats CCC(AAAACCCC)n, similar to those in spirotrichous ciliates such as Euplotes, Sterkiella (Oxytricha) and Stylonychia. Per sequenced chromosome we found evidence for either a single protein-coding gene, a single tRNA, or the complete ribosomal RNAs cluster. Hence the chromosomes appear to encode single transcripts. In the short subtelomeric regions we identified a few overrepresented motifs that could be involved in gene regulation, but there is no consensus polyadenylation site. The introns are short (21–29 nucleotides), and a significant fraction (1/3) of the tiny introns is conserved in the distantly related ciliate Paramecium tetraurelia. As has been observed in P. tetraurelia, the N. ovalis introns tend to contain in-frame stop codons or have a length that is not dividable by three. This pattern causes premature termination of mRNA translation in the event of intron retention, and potentially degradation of unspliced mRNAs by the nonsense-mediated mRNA decay pathway. The combination of short leaders, tiny introns and single genes leads to very minimal macronuclear chromosomes. The smallest we identified contained only 150 nucleotides.
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影响因子：
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