Sarkar Md Abdur Rauf, Sarkar Salim, Islam Md Shohelul, Zohra Fatema Tuz, Rahman Shaikh Mizanur
Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh.
Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh.
Genomics Inform. 2023 Sep;21(3):e36. doi: 10.5808/gi.23007. Epub 2023 Sep 27.
The LIM domain-containing proteins are dominantly found in plants and play a significant role in various biological processes such as gene transcription as well as actin cytoskeletal organization. Nevertheless, genome-wide identification as well as functional analysis of the LIM gene family have not yet been reported in the economically important plant sorghum (Sorghum bicolor L.). Therefore, we conducted an in silico identification and characterization of LIM genes in S. bicolor genome using integrated bioinformatics approaches. Based on phylogenetic tree analysis and conserved domain, we identified five LIM genes in S. bicolor (SbLIM) genome corresponding to Arabidopsis LIM (AtLIM) genes. The conserved domain, motif as well as gene structure analyses of the SbLIM gene family showed the similarity within the SbLIM and AtLIM members. The gene ontology (GO) enrichment study revealed that the candidate LIM genes are directly involved in cytoskeletal organization and various other important biological as well as molecular pathways. Some important families of regulating transcription factors such as ERF, MYB, WRKY, NAC, bZIP, C2H2, Dof, and G2-like were detected by analyzing their interaction network with identified SbLIM genes. The cis-acting regulatory elements related to predicted SbLIM genes were identified as responsive to light, hormones, stress, and other functions. The present study will provide valuable useful information about LIM genes in sorghum which would pave the way for the future study of functional pathways of candidate SbLIM genes as well as their regulatory factors in wet-lab experiments.
含LIM结构域的蛋白质主要存在于植物中，在基因转录以及肌动蛋白细胞骨架组织等各种生物过程中发挥重要作用。然而，在经济作物高粱（Sorghum bicolor L.）中，尚未有关于LIM基因家族的全基因组鉴定及功能分析的报道。因此，我们利用综合生物信息学方法，对高粱基因组中的LIM基因进行了电子鉴定和特征分析。基于系统发育树分析和保守结构域，我们在高粱基因组中鉴定出了五个与拟南芥LIM（AtLIM）基因相对应的LIM基因（SbLIM）。SbLIM基因家族的保守结构域、基序以及基因结构分析表明，SbLIM成员与AtLIM成员具有相似性。基因本体（GO）富集研究表明，候选LIM基因直接参与细胞骨架组织以及各种其他重要的生物学和分子途径。通过分析与已鉴定的SbLIM基因的相互作用网络，检测到了一些重要的转录因子调控家族，如ERF、MYB、WRKY、NAC、bZIP、C2H2、Dof和G2-like。与预测的SbLIM基因相关的顺式作用调控元件被鉴定为对光、激素、胁迫和其他功能有响应。本研究将为高粱中LIM基因提供有价值的信息，这将为未来在湿实验室实验中研究候选SbLIM基因及其调控因子的功能途径铺平道路。
