Genome Wide Identification and Expression Profiling Indicate Expansion of Family I84 Protease Inhibitor via Gene Tandem Duplication and Divergence in Razor Clam Sinonovacula constricta.
Genome Wide Identification and Expression Profiling Indicate Expansion of Family I84 Protease Inhibitor via Gene Tandem Duplication and Divergence in Razor Clam Sinonovacula constricta.
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DOI：
10.3389/fimmu.2022.907274
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发表时间：
2022
影响因子：
7.3
通讯作者：
Xue, Qinggang
中科院分区：
文献类型：
--
作者：
Liu, Sheng;Liu, Youli;Lu, Jiali;Mao, Jinxia;Lin, Zhihua;Xue, Qinggang
关键词：
I84 家族蛋白酶抑制剂代表了 MEROPS 肽酶数据库中的一个新家族，并且可能对于软体动物宿主防御来说是独一无二的。在之前的研究中，从缢蛏蛤中报道了 I84 科的两个成员 scSI-1 和 scSI-2。在本研究中，通过全基因组序列分析鉴定了另外 12 个基因，分别命名为 scSI-3 至 scSI-14。其中，10 个基因被预测具有信号序列，但 1 个基因（scSI-7）没有。此外，一个序列（scSI-14）可能编码一种过早终止的肽。预测的成熟肽与之前报道的家族成员具有共同的特征，包括 12 个保守的半胱氨酸残基、等电点为 4.98 至 6.11、分子量为 7.1 至 9.3 kDa。在 13 个预测的成熟肽（scSI-14 除外）中表征了四个基序，它们共享 2 至 4 个保守的半胱氨酸残基，可能分别形成两个包含 6 个半胱氨酸残基的功能域。在基因组水平上，所有14个蛏子家族I84基因都被组织成3个外显子和2个内含子；其中 13 个聚集在 3 条独立染色体上 3 个 100 kb 的区域，表明相关基因存在串联重复。预计所有 14 个基因的启动子区域共享一些转录因子结合位点，特别是那些对病理和生理刺激有反应的位点，但没有发现共享的基序。分析还揭示了基因之间表达模式的差异。串联重复基因对中的一个基因通常表现出比另一个基因更高的表达水平，而非串联重复基因在表达水平上表现出更高程度的相关性。此外，在副溶血性弧菌攻击后，14个基因中的8个在耐受弧菌的蛤中表现出比不耐受的蛤中更高的表达水平。这些结果产生了有关 I84 家族蛋白酶抑制剂在 S. constricta 中进化的重要信息。
Family I84 protease inhibitors represent a novel family in the MEROPS peptidase database and are likely unique for molluscan host defense. Two Family I84 members, scSI-1 and scSI-2, were reported from the razor clam Sinonovacula constricta in a previous research. In the present study, 12 additional genes, named scSI-3 to scSI-14, were identified via genome wide sequence analyses. Among them, 10 genes were predicted to have a signal sequence, but one (scSI-7) was not. Besides, one sequence (scSI-14) was likely to encode a prematurely terminated peptide. The predicted mature peptides shared characteristics including 12 conserved cysteine residues, isoelectric points of 4.98 to 6.11, and molecular weights of 7.1 to 9.3 kDa with previously reported family members. Four motifs were characterized in 13 predicted mature peptides (with exception of scSI-14), which shared two to four conserved cysteine residues, are possibly to form two functional domain comprised 6 cysteine residues, respectively. At genomic level, all the 14 razor clam Family I84 genes were organized into 3 exons and 2 introns; 13 of them clustered in 3 regions of 100 kb on 3 separate chromosomes, suggesting tandem duplications of related genes. The promoter region of all the 14 genes was predicted to share some transcription factor binding sites, in particular those responsive to pathological and physiological stimuli, but no shared motifs were identified. Analyses also revealed differences in expression patterns among the genes. One gene in a tandem duplicated gene pairs usually showed a higher expression level than the other whereas non-tandem duplicated genes exhibited a higher degree of correlation in expression level. In addition, 8 of the 14 genes demonstrated higher level of expression in Vibrio tolerant clams than in non-tolerant clams following challenges with Vibrio parahaemolyticus. These results generated important information about the evolution of Family I84 protease inhibitors in S. constricta.
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影响因子：
3.7
作者：
McDowell IC;Nikapitiya C;Aguiar D;Lane CE;Istrail S;Gomez-Chiarri M
通讯作者：
Gomez-Chiarri M
DOI：
10.1101/sqb.1987.052.01.062
发表时间：
1987-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
LASKOWSKI, M;KATO, I;WHATLEY, HE
通讯作者：
WHATLEY, HE
影响因子：
1.4
作者：
Lu, Jiali;Liu, Sheng;Xue, Qinggang
通讯作者：
Xue, Qinggang
影响因子：
64.8
作者：
Papp, B;Pál, C;Hurst, LD
通讯作者：
Hurst, LD
影响因子：
10.7
作者：
Gu, ZL;Cavalcanti, A;Li, WH
通讯作者：
Li, WH