Popova L G, Belyaev D V, Shuvalov A V, Yurchenko A A, Matalin D A, Khramov D E, Orlova Y V, Balnokin Y V
Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276 Russia.
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199034 Russia.
Mol Biol (Mosk). 2018 Jul-Aug;52(4):601-615. doi: 10.1134/S002689841804016X.
De novo assembled transcriptomes of the marine microalga Dunaliella tertiolecta (Chlorophyta) were analyzed. Transcriptome assemblies were performed using short-read RNA-seq data deposited in the SRA database (DNA and RNA Sequence Read Archive, NCBI). A merged transcriptome was assembled using a pooled RNA-seq data set. The goal of the study was in silico identification of nucleotide sequences encoding P-type ATPases in D. tertiolecta transcriptomes. P-type ATPases play a considerable role in the adaptation of an organism to a variable environment, and this problem is particularly significant for microalgae inhabiting an environment with an unstable ionic composition. Particular emphasis was given to searching for a sequence coding Na^(+)-ATPase. This enzyme is expected to function in the plasma membrane of D. tertiolecta like in some marine algae, in particular, in the closely related alga Dunaliella maritima. An ensemble of 12 P-type ATPases consisting of members belonging to the five main subfamilies of the P-type ATPase family was revealed in the assembled transcriptomes. The genes of the following P-type ATPases were found: (1) heavy metal ATPases (subfamily PIB); (2) Ca^(2+)-ATPases of SERCA type (subfamily P2A); (3) H^(+)-ATPases (subfamily P3); (4) phospholipid-transporting ATPases (flippases) (subfamily P4); (5) cation-transporting ATPases of uncertain specificities (subfamily P5). The presence of functional Na^(+)-ATPases in marine algae is presently undoubted. However, contrary to expectations, we failed to find a nucleotide sequence encoding a protein that could unequivocally be considered a Na^(+)-ATPase. Further study is necessary to elucidate the roles of in silico revealed D. tertiolecta ATPases in Na^(+) transport.
对海洋微藻杜氏盐藻（绿藻门）的从头组装转录组进行了分析。转录组组装使用了存于SRA数据库（DNA和RNA序列读取存档库，NCBI）中的短读长RNA测序数据。利用合并的RNA测序数据集组装了一个合并转录组。该研究的目的是在杜氏盐藻转录组中通过计算机模拟鉴定编码P型ATP酶的核苷酸序列。P型ATP酶在生物体适应多变环境中发挥着重要作用，对于生活在离子组成不稳定环境中的微藻来说，这个问题尤为重要。特别着重于寻找编码Na⁺-ATP酶的序列。预计这种酶在杜氏盐藻的质膜中发挥作用，就像在一些海藻中一样，特别是在亲缘关系较近的海藻杜氏盐藻中。在组装的转录组中发现了一组由12个P型ATP酶组成的集合，它们属于P型ATP酶家族的五个主要亚家族。发现了以下P型ATP酶的基因：（1）重金属ATP酶（PIB亚家族）；（2）SERCA型Ca²⁺-ATP酶（P2A亚家族）；（3）H⁺-ATP酶（P3亚家族）；（4）磷脂转运ATP酶（翻转酶）（P4亚家族）；（5）特异性不确定的阳离子转运ATP酶（P5亚家族）。目前，海藻中存在功能性Na⁺-ATP酶是毋庸置疑的。然而，与预期相反，我们未能找到一个明确编码可被视为Na⁺-ATP酶的蛋白质的核苷酸序列。需要进一步研究以阐明通过计算机模拟揭示的杜氏盐藻ATP酶在Na⁺转运中的作用。
