Prediction of IER5 structure and function using a bioinformatics approach

Abstract

Immediate-early response gene 5 (IER5) is a gene involved in the regulation of the cell cycle, and its structure and function have been investigated by bioinformatics analyses. The present study determined the sites of promoter methylation and gene ontology (GO) annotations associated with IER5. In addition, we conducted a prediction analysis to determine the physical and chemical properties, hydrophobicity/hydrophilicity, posttranslational modification, subcellular localization, transmembrane structure, signal peptide and secondary and tertiary structures of IER5. One CpG island and several methylated sites were identified close to the promoter of IER5 . The GO analysis suggested that IER5 could bind ions and proteins that were mainly associated with metabolic processes. IER5 comprised 327 amino acids and was reported to be an unstable hydrophilic protein with an isoelectric point of 4.91. A total of 18 O-glycosylation sites and 22 phosphorylation sites were identified within this protein. The subcellular localization of IER5 was mainly in the nucleus, and its main secondary structural element was the α-helix. Bioinformatic analyses of the features of IER5 may improve understanding of its structure and function; however, experimental verification is required.

Genes with evidence of positive selection as potentially related to coloniality and the evolution of morphological features among the lophophorates and entoprocts

“…A combined functional synthesis gathered for all of the cellular and developmentally related genes listed here results in some commonalities among their respective roles such as immune response (CNPY4; Takahashi et al, 2007), mRNA processing and translation (EIF1, EIF1AD, and TARDBP; Buratti & Baralle, 2008;Mitchell & Lorsch, 2008;J. Yu & Marintchev, 2018), cell cycle progression, cell proliferation, and cell growth (GADD45GIP1, GHITM, IER5, EIF1, EIF1AD, and USF2; Fujimi & Aruga, 2008;Kwon et al, 2009;Sehrawat et al, 2019;Xiong, Jiang, Liu, Zhou, & Ding, 2019;J. Yu & Marintchev, 2018;W.…”

“…As the other tree topologies shown in Figure 4d–f provide support for a clade that includes all ectoproct and bryozoan species, these genes may be associated with the differentiation of multiciliated cells. A combined functional synthesis gathered for all of the cellular and developmentally related genes listed here results in some commonalities among their respective roles such as immune response ( CNPY4 ; Takahashi et al, 2007), mRNA processing and translation ( EIF1 , EIF1AD , and TARDBP ; Buratti & Baralle, 2008; Mitchell & Lorsch, 2008; J. Yu & Marintchev, 2018), cell cycle progression, cell proliferation, and cell growth ( GADD45GIP1 , GHITM, IER5 , EIF1, EIF1AD , and USF2 ; Fujimi & Aruga, 2008; Kwon et al, 2009; Sehrawat et al, 2019; Xiong, Jiang, Liu, Zhou, & Ding, 2019; J. Yu & Marintchev, 2018; W. Yu et al, 2020), and the development of the nervous system and cilia ( CFAP126 , RSPH9 , USF2 , SEC13 , and VEGFA ; Erskine et al, 2017; Fujimi & Aruga, 2008; Gegg et al, 2014; Niu et al, 2014; Sedykh et al, 2016).…”

Genome-Wide Identification and Expression Analysis of Cysteine-Rich Polycomb-like Protein (CPP) Gene Family in Tomato

“…Based on these data, six SlCPP genes were identified in the whole tomato genome in this study by bioinformatics analysis based on the characteristic sequences of the CRC structural domain unique to the CPP transcription factor family. The results of physicochemical property analysis showed that all SlCPP proteins were hydrophilic proteins, differing from those in other species, suggesting that not all members of the CPP transcription factor family are hydrophilic or hydrophobic proteins and that they may perform different functions in different species [ 30 ].…”

p53-Dependent Cytoprotective Mechanisms behind Resistance to Chemo-Radiotherapeutic Agents Used in Cancer Treatment

“…IERs are of two types: fast-kinetic IERs whose transcription peaks in 30 min and returns to baseline by two hours, and slow-kinetic IERs whose transcription has a greater lag and persist longer. IER5 , a novel member of the slow-kinetics IERs, is an intronless gene consisting of 2110 nucleotides that encodes a highly proline-rich nuclear protein of 327 amino acids (33.7 kDa) containing a PEST-like sequence and multiple phosphorylation and O-glycosylation sites [ 66 , 67 ]. IER5 has two nuclear localization sequences (NLS) between amino acids 217–244.…”

“…The IER5 gene promoter contains two Ets-1 sites and multiple AP-1 and Sp1 sites. Its N-terminal domain consists of 49 amino acids and is 57% identical and 90% similar to the N-terminal domain of IER2 [ 66 , 67 ].…”