Multiple roles of the coding sequence 5′ end in gene expression regulation

The codon composition of the coding sequence''s (ORF) 5′ end first few dozen codons is known to be distinct to that of the rest of the ORF. Various explanations for the unusual codon distribution in this region have been proposed in recent years, and include, among others, novel regulatory mechanisms of translation initiation and elongation. However, due to the fact that many overlapping regulatory signals are suggested to be associated with this relatively short region, its research is challenging. Here, we review the currently known signals that appear in this region, the theories related to the way they regulate translation and affect the organismal fitness, and the debates they provoke.     

DNA sequence analysis of the rat RT1. B α gene

The major histocompatibility complex (MHC) of the rat (RT1 complex) encodes two sets of class II molecules referred to as RT1.B and RT1.D. The RT1. B gene was isolated for a Sprague-Dawley (RT1^b) rat genomic library using a rat RT1.B chain cDNA as a hybridization probe. The coding and the majority of the intron DNA sequence was determined. The structure of the RT1. B gene is equivalent to that of H-2 and HLA chain genes. Comparison of the nucleotide and predicted amino acid sequences of the RT1.B gene with those of the H-2 and HLA genes revealed a high degree of overall sequence conservation. However, two regions of the first external domain (l), residues 19–23 and 45–78, exhibit marked sequence variation. Two blocks of conserved nucleotide sequence were identified in the 5 promoter region of the RT1. B gene that have been described in all MHC class II genes sequenced to date. These conserved sequences may be involved in the coordinate regulation of expression of class II genes. The cloned RT1.B gene was efficiently transcribed when transfected to mouse L cells.     

The regulation of the UCH-L1 gene by transcription factor NF-κB in podocytes

In kidney, the ubiquitin carboxy-terminal hydrolase 1 (UCH-L1) is involved in podocyte injury and proteinuria but details of the mechanism underlying its regulation are not known. Activation of NF-κB is thought to be the predominant risk factor for kidney disease; therefore, it is postulated that UCH-L1 may be one of the NF-κB target genes. In this study, we investigated the involvement of NF-κB activation in the regulation of UCH-L1 expression and the function of murine podocytes. Stimulation of podocytes with the cytokines TNF-α and IL-1β up-regulated UCH-L1 expression rapidly at the mRNA and protein levels and the NF-κB-specific inhibitor pyrrolidine dithiocarbamate resulted in down-regulation. NF-κB up-regulates UCH-L1 via binding the ? 300 bp and ? 109 bp sites of its promoter, which was confirmed by the electrophoretic mobility shift assay of DNA–nuclear protein binding. In the renal biopsy from lupus nephritis patients, the expressions of NF-κB and UCH-L1 increased in immunohistochestry staining and were positively correlated. Activation of NF-κB up-regulates UCH-L1 expression following changing of other podocytes molecules, such as nephrin and snail. These results suggest that activation of the NF-κB signaling pathway could be the major pathogenesis to up-regulate UCH-L1 in podocyte injury, followed by the turnover of other molecules, which might result in morphological changes and dysfunction of podocytes. This work help us to understand the effect of NF-κB on specific target molecules of podocytes, and suggest that targeting the NF-κB–UCH-L1 interaction could be a novel therapeutic strategy for the treatment of podocyte lesions and proteinuria.     

Role of α-CGRP in the regulation of neurotoxic responses induced by kainic acid in mice

Kainic acid (KA) is an excitatory and neurotoxic substance. The role of α-calcitonin gene-related peptide (α-CGRP) in the regulation of KA-induced hippocampal neuronal cell death was investigated in the present study. The intracerebroventricular (i.c.v.) administration with KA (0.07 μg) increased hippocampal α-CGRP mRNA level in ICR mice. The α-CGRP mRNA level began to increase at 1 h, reached at maximal level at 6 and 12 h, and returned to the control level by 24 h after i.c.v. administration with KA. In addition, KA-induced hippocampal CA3 neuronal death in C57BL6 (wild type) group was more pronounced compared to KA-induced hippocampal CA3 pyramidal cell death in α-CGRP knock-out (KO) group. Furthermore, sumatriptan, a CGRP releasing inhibitor, significantly protected the pyramidal cell death in CA3 hippocampal region induced by KA administered i.c.v. in ICR mice. Our results suggest that α-CGRP may play an important role in the regulation of KA-induced pyramidal cell death in CA3 region of the hippocampus.     

Bypass of N²-ethylguanine by human DNA polymerase κ

The efficiency and fidelity of nucleotide incorporation and next-base extension by DNA polymerase (pol) κ past N(2)-ethyl-Gua were measured using steady-state and rapid kinetic analyses. DNA pol κ incorporated nucleotides and extended 3' termini opposite N(2)-ethyl-Gua with measured efficiencies and fidelities similar to that opposite Gua indicating a role for DNA pol κ at the insertion and extension steps of N(2)-ethyl-Gua bypass. The DNA pol κ was maximally activated to similar levels by a twenty-fold lower concentration of Mn(2+) compared to Mg(2+). In addition, the steady state analysis indicated that high fidelity DNA pol κ-catalyzed N(2)-ethyl-Gua bypass is Mg(2+)-dependent. Strikingly, Mn(2+) activation of DNA pol κ resulted in a dramatically lower efficiency of correct nucleotide incorporation opposite both N(2)-ethyl-Gua and Gua compared to that detected upon Mg(2+) activation. This effect is largely governed by diminished correct nucleotide binding as indicated by the high K(m) values for dCTP insertion opposite N(2)-ethyl-Gua and Gua with Mn(2+) activation. A rapid kinetic analysis showed diminished burst amplitudes in the presence of Mn(2+) compared to Mg(2+) indicating that DNA pol κ preferentially utilizes Mg(2+) activation. These kinetic data support a DNA pol κ wobble base pairing mechanism for dCTP incorporation opposite N(2)-ethyl-Gua. Furthermore, the dramatically different polymerization efficiencies of the Y-family DNA pols κ and ι in the presence of Mn(2+) suggest a metal ion-dependent regulation in coordinating the activities of these DNA pols during translesion synthesis.     

High-level expression of a polypeptides encoded by a large segment of the envelope gene of HIV-1 in E. coli by directed evolution

A random mutagenesis library of gp120-801 (a large segment of the envelope protein gene of HIV-1) was constructed using error-prone PCR and DNA shuffling methods, and one mutant of gp120-801 was selected from this library using a green fluorescent protein (GFP) fusion vector. After being cloned into pEX31b and expressed in E. coli, the expressed fusion protein reached to 15% of total bacterial proteins for the mutant but was just 1–2% for the wild type.     

Role of the Polymerase ? sub-unit DPB2 in DNA replication,cell cycle regulation and DNA damage response in Arabidopsis

Faithful DNA replication maintains genome stability in dividing cells and from one generation to the next. This is particularly important in plants because the whole plant body and reproductive cells originate from meristematic cells that retain their proliferative capacity throughout the life cycle of the organism. DNA replication involves large sets of proteins whose activity is strictly regulated, and is tightly linked to the DNA damage response to detect and respond to replication errors or defects. Central to this interconnection is the replicative polymerase DNA Polymerase ϵ (Pol ϵ) which participates in DNA replication per se, as well as replication stress response in animals and in yeast. Surprisingly, its function has to date been little explored in plants, and notably its relationship with DNA Damage Response (DDR) has not been investigated. Here, we have studied the role of the largest regulatory sub-unit of Arabidopsis DNA Pol ϵ: DPB2, using an over-expression strategy. We demonstrate that excess accumulation of the protein impairs DNA replication and causes endogenous DNA stress. Furthermore, we show that Pol ϵ dysfunction has contrasting outcomes in vegetative and reproductive cells and leads to the activation of distinct DDR pathways in the two cell types.     

Transaminase encoded by NCgl2515 gene of Corynebacterium glutamicum ATCC13032 is involved in γ-aminobutyric acid decomposition

Corynebacterium glutamicum that expresses an exogenous l-glutamate decarboxylase (GAD) gene can synthesize γ-aminobutyric acid (GABA). GABA is decomposed to succinic semialdehyde (SSA) by GABA transaminase (GABA-T) and to succinate thereafter by SSA dehydrogenase (SSADH). However, deletion of the gabT gene encoding GABA-T could not prevent GABA from decomposing at neutral pH. In this study, an additional transaminase gene, NCgl2515, was deleted in a gabT-deleted GAD strain, and GABA fermentation in this gabT NCgl2515-deleted GAD strain was investigated. GABA concentration remained at 22.5–24.0 g/L when pH was maintained at 7.5–8.0, demonstrating that GABA decomposition was reduced. Activity assay indicated that unlike GabT, which exhibits high GABA-T activity (1.34 ± 0.06 U/mg) and utilizes only α-ketoglutarate as amino acceptor, the purified NCgl2515 protein exhibits very low GABA-T activity (approximately 0.03 U/mg) only when coupled with the SSADH, GabD, but can utilize both α-ketoglutarate and pyruvate as amino acceptor. The optimum pH for coupled NCgl2515–GabD was 8.0, similar to that of GabT (7.8). Therefore, NCgl2515 has weak GABA-T activity and is involved in GABA decomposition in C. glutamicum. Deletion of gabT and NCgl2515 could effectively reduce GABA decomposition at neutral pH.