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Molecular Biology and Bioinformatics in Industrial Microbiology and Biotechnology
Published in Nduka Okafor, Benedict C. Okeke, Modern Industrial Microbiology and Biotechnology, 2017
Nduka Okafor, Benedict C. Okeke
Regions of DNA that encode proteins are first transcribed into messenger RNA and then translated into protein. By examining the DNA sequence alone, we can determine the putative sequence of amino acids that will appear in the final protein. During translation, codons of three nucleotides determine which amino acid will be added next in the growing protein chain. On mRNA start codon is usually AUG, while the stop codons are UAA, UAG, and UGA. The open reading frame (ORF) is that portion of a DNA segment which will putatively code for a protein; it begins with a start codon and ends with a stop codon. Once a gene has been sequenced, it is important to determine the correct open reading frame. Every region of DNA has six possible reading frames, three in each direction because a codon consists of three nucleotides. The reading frame that is used determines which amino acids will be encoded by a gene. Typically, only one reading frame is used in translating a gene (in eukaryotes), and this is often the longest open reading frame. Once the open reading frame is known, the DNA sequence can be translated into its corresponding amino acid sequence.
Glossary of scientific and technical terms in bioengineering and biological engineering
Published in Megh R. Goyal, Scientific and Technical Terms in Bioengineering and Biological Engineering, 2018
Reading frame is a series of triplets beginning from a specific nucleotide. Each triplet is represented by a single amino acid in the protein synthesized. The reading frame defines which sets of three nucleotides are read as triplets in the DNA, and hence as codons in the corresponding mRNA; this is determined by the initiation codon, AUG. Thus the sequence AUGGCAAAAUUUCCC would read as AUG/GCA/AAA/UUU/CCC/, and not as A/UGC/CAA/AAU/UUC/CC. Depending on where one begins, each DNA strand contains three different reading frames.
Enolase, a cadmium resistance related protein from hyperaccumulator plant Phytolacca americana, increase the tolerance of Escherichia coli to cadmium stress
Published in International Journal of Phytoremediation, 2023
Le Zhao, Yunhao Zhu, Min Wang, Yongguang Han, Jiao Xu, Weisheng Feng, Xiaoke Zheng
The sequence of PaENO gene was submitted to the NCBI GenBank and aligned with the Nr (non-redundant) protein database by blastx (Boratyn et al. 2013). Then, the open reading frame (ORF) was searched by the NCBI ORF Finder. The molecular weight (MW) and isoelectric point (pI) of PaENO were predicted by the ProtParam tool, and the InterPro Scan was adopted to predict the conserved domains. The protein secondary structure was predicted by Predict Protein, and three-dimensional homologous modeling of PaENO was performed through SWISS-MODEL and visualized with PyMOL 2.3.2 (Mooers 2020). SignalP 5.0, TargetP 2.0, and TMHMM 2.0 were employed for prediction of signal peptide, subcellular localization, and transmembrane region, respectively. DNAMAN software was used for the multiple sequence alignment of ENOs from different plants. The phylogenetic tree was constructed using MEGA7 neighbor-joining (NJ) method (Kumar et al. 2016), and visualized with the online tool Evolviewv2 (He et al. 2016).
Molecular and biochemical characterizations of a new cold-active and mildly alkaline β-Mannanase from Verrucomicrobiae DG1235
Published in Preparative Biochemistry & Biotechnology, 2021
Huifang Xie, Chun Kin Kingsley Poon, Hanyan Liu, Dan Wang, Jiangke Yang, Zhenggang Han
According to genome annotation, the open-reading frame of ManDG1235 consists of 1152 nucleotides, which encode a protein with 383 amino acid residues (GenBank accession number: EDY81501.1). The deduced amino acid sequence has a signal peptide of 23 amino acids, which was predicted by the SignalP5.0 server (D = 0.754, D-cutoff = 0.570). BLASTp search indicated that full-length ManDG1235 had the highest sequence consistency with the putative GH1 protein from Gracilimonas mengyeensis (GenBank accession number: WP_142454179.1) and the putative β-mannanase (man26C, GenBank accession number: KAF0095511.1) from Punicoccaceae 5H, at 58.84 and 58.42%, respectively. A phylogenetic tree including those well-characterized β-mannanases indicated that ManDG1235 belongs to the GH26 family (Figure 1). ManDG1235 is well-related to CjMan26C from Cellvibrio japonicus Ueda107 (GenBank accession number: ACE84009.1), with an amino acid sequence identity of 49.2% (Figure 1).
Novel attacin from Hermetia illucens: cDNA cloning, characterization, and antibacterial properties
Published in Preparative Biochemistry and Biotechnology, 2019
The open reading frame (ORF) of the HI-attacin gene was amplified by reverse transcription-polymerase chain reaction (RT-PCR) using HI-attacin BamHI and HI-attacin XhoI primers (Table 1). The amplified DNA fragment was cloned into pET21a vector (Novagen) and its sequence was confirmed by nucleotide sequencing. The competent cells of E. coli Rosetta2 pLysS (Novagen) were transformed with the vector construct for expression of the recombinant HI-attacin (rHI-attacin). A single transformed colony was grown in 200 mL Luria-Bertani (LB) medium containing 100 µg/mL ampicillin at 37 °C for 12 h in a VS-8480S shaking incubator (Vision Scientific Co., Korea). When the optical density of the culture at 600 nm reached 0.4–0.5, the expression of rHI-attacin was induced by adding isopropyl-β-d-thiogalactopyranoside (IPTG) to a final concentration of 0.3 mM and further incubating at 37 °C for 2 h. The culture (700 µL) was then centrifugedand the bacterial pellet that was obtained was lysed in 100 µL denaturing buffer. The protein extract (10 µL) was electrophoresed on a 12% sodium dodecylsulfate-polyacrylamide gel (10 × 8 × 0.075 cm) under reducing conditions at a constant voltage of 120 V. The gel was visualized after staining with Coomassie brilliant blue R-250 (Sigma).