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The complete mitogenome of the New Zealand freshwater crayfish Paranephrops planifrons White 1842 (Crustacea: Decapoda: Parastacidae)

Lee YP, Gan HM, Tan MH, Lys I, Page R, Dias Wanigasekera B, et al.

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 09;27(5):3333-4.
PMID: 25707411 DOI: 10.3109/19401736.2015.1018209

The mitogenome of Paranephrops planifrons, was obtained by next generation sequencing. This crayfish has a mitochondrial genome of 16,174 base pairs with 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs (tRNA), and a non-coding AT-rich region of 771 bp. The P. planifrons nucleotide composition is: 33.63% for T, 21.92% for C, 34.46% for A, and 9.98% for G and has a 68.09% AT bias. While the mitogenome gene order for this species is consistent with aspects of the highly distinctive parastacid crayfish mitogenome gene arrangement, it has a novel gene order involving the rearrangements of a protein coding and several tRNA genes.

Matched MeSH terms: Codon
The complete mitogenome of the giant clam Tridacna squamosa (Heterodonta: Bivalvia: Tridacnidae)

Gan HM, Gan HY, Tan MH, Penny SS, Willan RC, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 09;27(5):3220-1.
PMID: 25648928 DOI: 10.3109/19401736.2015.1007355

The complete mitochondrial genome of the commercially and ecologically important and internationally vulnerable giant clam Tridacna squamosa was recovered by genome skimming using the MiSeq platform. The T. squamosa mitogenome has 20,930 base pairs (62.35% A+T content) and is made up of 12 protein-coding genes, 2 ribosomal subunit genes, 24 transfer RNAs, and a 2594 bp non-coding AT-rich region. The mitogenome has a relatively large insertion in the atp6 gene. This is the first mitogenome to be sequenced from the genus Tridacna, and the family Tridacnidae and represents a new gene order.

Matched MeSH terms: Codon
More evolution underground: Accelerated mitochondrial substitution rate in Australian burrowing freshwater crayfishes (Decapoda: Parastacidae)

Gan HM, Tan MH, Lee YP, Schultz MB, Horwitz P, Burnham Q, et al.

Mol Phylogenet Evol, 2018 01;118:88-98.
PMID: 28966124 DOI: 10.1016/j.ympev.2017.09.022

To further understand the evolutionary history and mitogenomic features of Australia's highly distinctive freshwater crayfish fauna, we utilized a recently described rapid mitogenome sequencing pipeline to generate 24 new crayfish mitogenomes including a diversity of burrowing crayfish species and the first for Astacopsis gouldi, the world's largest freshwater invertebrate. Whole mitogenome-based phylogeny estimates using both Bayesian and Maximum Likelihood methods substantially strengthen existing hypotheses for systematic relationships among Australian freshwater crayfish with evidence of pervasive diversifying selection and accelerated mitochondrial substitution rate among the members of the clade representing strongly burrowing crayfish that may reflect selection pressures for increased energy requirement for adaptation to terrestrial environment and a burrowing lifestyle. Further, gene rearrangements are prevalent in the burrowing crayfish mitogenomes involving both tRNA and protein coding genes. In addition, duplicated control regions were observed in two closely related Engaeus species, together with evidence for concerted evolution. This study significantly adds to the understanding of Australian freshwater crayfish evolutionary relationships and suggests a link between mitogenome evolution and adaptation to terrestrial environments and a burrowing lifestyle in freshwater crayfish.

Matched MeSH terms: Codon
Fulltext Codon usage and codon pair patterns in non-grass monocot genomes

Mazumdar P, Binti Othman R, Mebus K, Ramakrishnan N, Ann Harikrishna J

Ann Bot, 2017 Nov 28;120(6):893-909.
PMID: 29155926 DOI: 10.1093/aob/mcx112

Background and Aims: Studies on codon usage in monocots have focused on grasses, and observed patterns of this taxon were generalized to all monocot species. Here, non-grass monocot species were analysed to investigate the differences between grass and non-grass monocots.
Methods: First, studies of codon usage in monocots were reviewed. The current information was then extended regarding codon usage, as well as codon-pair context bias, using four completely sequenced non-grass monocot genomes (Musa acuminata, Musa balbisiana, Phoenix dactylifera and Spirodela polyrhiza) for which comparable transcriptome datasets are available. Measurements were taken regarding relative synonymous codon usage, effective number of codons, derived optimal codon and GC content and then the relationships investigated to infer the underlying evolutionary forces.
Key Results: The research identified optimal codons, rare codons and preferred codon-pair context in the non-grass monocot species studied. In contrast to the bimodal distribution of GC3 (GC content in third codon position) in grasses, non-grass monocots showed a unimodal distribution. Disproportionate use of G and C (and of A and T) in two- and four-codon amino acids detected in the analysis rules out the mutational bias hypothesis as an explanation of genomic variation in GC content. There was found to be a positive relationship between CAI (codon adaptation index; predicts the level of expression of a gene) and GC3. In addition, a strong correlation was observed between coding and genomic GC content and negative correlation of GC3 with gene length, indicating a strong impact of GC-biased gene conversion (gBGC) in shaping codon usage and nucleotide composition in non-grass monocots.
Conclusion: Optimal codons in these non-grass monocots show a preference for G/C in the third codon position. These results support the concept that codon usage and nucleotide composition in non-grass monocots are mainly driven by gBGC.

Matched MeSH terms: Codon/genetics*
Fulltext Hemolytic anemia and distal renal tubular acidosis in two Indian patients homozygous for SLC4A1/AE1 mutation A858D

Shmukler BE, Kedar PS, Warang P, Desai M, Madkaikar M, Ghosh K, et al.

Am J Hematol, 2010 Oct;85(10):824-8.
PMID: 20799361 DOI: 10.1002/ajh.21836

Familial distal renal tubular acidosis (dRTA) can be caused by mutations in the Cl2/HCO32 exchanger of the renal Type A intercalated cell, kidney AE1/SLC4A1. dRTA-associated AE1 mutations have been reported in families from North America, Europe, Thailand, Malaysia, Papua-New Guinea, Taiwan, and the Philippines, but not India. The dRTA mutation AE1 A858D has been detected only in the context of compound heterozygosity. We report here two unrelated Indian patients with combined hemolytic anemia and dRTA who share homozygous A858D mutations of the AE1/SLC4A1 gene. The mutation creates a novel restriction site that is validated for diagnostic screening.

Matched MeSH terms: Codon/genetics
Fulltext Engineering and Validation of a Vector for Concomitant Expression of Rare Transfer RNA (tRNA) and HIV-1 nef Genes in Escherichia coli

Mualif SA, Teow SY, Omar TC, Chew YW, Yusoff NM, Ali SA

PLoS One, 2015;10(7):e0130446.
PMID: 26147991 DOI: 10.1371/journal.pone.0130446

Relative ease in handling and manipulation of Escherichia coli strains make them primary candidate to express proteins heterologously. Overexpression of heterologous genes that contain codons infrequently used by E. coli is related with difficulties such as mRNA instability, early termination of transcription and/or translation, deletions and/or misincorporation, and cell growth inhibition. These codon bias -associated problems are addressed by co-expressing ColE1-compatible, rare tRNA expressing helper plasmids. However, this approach has inadequacies, which we have addressed by engineering an expression vector that concomitantly expresses the heterologous protein of interest, and rare tRNA genes in E. coli. The expression vector contains three (argU, ileY, leuW) rare tRNA genes and a useful multiple cloning site for easy in-frame cloning. To maintain the overall size of the parental plasmid vector, the rare tRNA genes replaced the non-essential DNA segments in the vector. The cloned gene is expressed under the control of T7 promoter and resulting recombinant protein has a C-terminal 6His tag for IMAC-mediated purification. We have evaluated the usefulness of this expression vector by expressing three HIV-1 genes namely HIV-1 p27 (nef), HIV-1 p24 (ca), and HIV-1 vif in NiCo21(DE3) E.coli and demonstrated the advantages of using expression vector that concomitantly expresses rare tRNA and heterologous genes.

Matched MeSH terms: Codon/genetics
Spectrum of germ-line RB1 gene mutations in Malaysian patients with retinoblastoma

Mohd Khalid MK, Yakob Y, Md Yasin R, Wee Teik K, Siew CG, Rahmat J, et al.

Mol Vis, 2015;21:1185-90.
PMID: 26539030

The availability of molecular genetic testing for retinoblastoma (RB) in Malaysia has enabled patients with a heritable predisposition to the disease to be identified, which thus improves the clinical management of these patients and their families. In this paper, we presented our strategy for performing molecular genetic testing of the RB1 gene and the findings from our first 2 years of starting this service.

Matched MeSH terms: Codon, Nonsense
Fulltext Investigation Trp64Arg polymorphism of the beta 3-adrenergic receptor gene in nonobese women with polycystic ovarian syndrome

Zangeneh FZ, Shoushtari MS, Shojaee S, Aboutorabi E

Int J Reprod Biomed, 2020 Mar;18(3):165-174.
PMID: 32309765 DOI: 10.18502/ijrm.v18i3.6712

Background: Polycystic ovary syndrome (PCOS) is a multifactorial and heterogeneous disease that has a potent inheritable component based on familial clustering. Despite many studies in the genetic field of PCOS, the genes that are involved in the causes of this syndrome have not been thoroughly investigated.
Objective: The purpose of this study was to establish the occurrence of the Trp64Arg polymorphism of beta3 adrenergic receptor in non-obese women with PCOS.
Materials and Methods: This cross-sectional study was performed on 100 women with PCOS and normal women as the control group in Imam Khomeini Hospital of Tehran in 2016-2017. Peripheral blood sample (2 cc) was obtained from two groups for genomic DNA based on the gene bank. Polymorphisms were genotyped by of using ADRB3 Trp64Arg. Then the DNA was extracted by genomic kiagen kit. The primer was analyzed for PCR based on gene bank by using Primer3 software and then confirmed by primer Blast tool at NCBI site to conformity to the beta-3 adrenergic receptor gene. The protein changes were assessment by the Clastal W software.
Results: The sequence analysis presented in NCBI, transcript variant 1, with the code NM_000025.2, shows changes in the amino acid sequence of exon 1 in women with PCOS. Polymorphism in the codon 64 encoding the amino acid tryptophan (W) occurred in the nucleotide c.T190C, which changed the nucleotide T to C and then the amino acid sequence of the tryptophan was altered to arginine pW64R.
Conclusion: T-C polymorphism is evident in the codon 64 of the adrenergic β3 receptor in patients with PCOS. Therefore, Beta3 adrenergic receptor gene polymorphism (Thr164Ile) associates with this syndrome in nonobese women.

Matched MeSH terms: Codon
Cloning of high activity xylanase gene from Bacillus pumilus PJ19

Hamzah A, Abdulrashid N

J. Biochem. Mol. Biol. Biophys., 2002 Oct;6(5):365-9.
PMID: 12385974

The xylanase gene from Bacillus pumilus PJ19 amplified by polymerase chain reaction (PCR) was cloned into pCRII vector and transformed into Escherichia coli strain INValphaF'. Starting from an ATG as an initiator codon, an open reading frame coding for 202 amino acids was obtained. The recombinant xylanase sequence showed a 96% homology with the xylanase sequence from B. pumilus IPO strain and had an estimated molecular weight of 22,474. Xylanase activity expressed by E. coli INValphaF' harboring the cloned gene was located primarily in the cytoplasmic fraction.

Matched MeSH terms: Codon/genetics
Fulltext The complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) from Peninsular Malaysia

Rosli N, Sitam FT, Rovie-Ryan JJ, Gan HM, Lee YP, Hartini Ithnin, et al.

Mitochondrial DNA B Resour, 2019 Jul 13;4(2):2535-2536.
PMID: 33365614 DOI: 10.1080/23802359.2019.1640085

Here, we present the first complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) inferred using next-generation sequencing. The mitogenome is 16,367 bp in length with the structural organization of a typical bovine mitochondrial arrangement comprising 13 protein-coding genes, 21 tRNAs, and 2 rRNAs. No internal stop codon was found in the protein-coding genes. Phylogenetic tree analysis revealed that Malayan gaur is more closely related to Burmese banteng instead of gaur.

Matched MeSH terms: Codon, Terminator
Identification of the genomic mutation in Epha4(rb-2J/rb-2J) mice

Mohd-Zin SW, Abdullah NL, Abdullah A, Greene ND, Cheah PS, Ling KH, et al.

Genome, 2016 Jul;59(7):439-48.
PMID: 27373307 DOI: 10.1139/gen-2015-0142

The EphA4 receptor tyrosine kinase is involved in numerous cell-signalling activities during embryonic development. EphA4 has the ability to bind to both types of ephrin ligands, the ephrinAs and ephrinBs. The C57BL/6J-Epha4rb-2J/GrsrJ strain, denoted Epha4(rb-2J/rb-2J), is a spontaneous mouse mutant that arose at The Jackson Laboratory. These mutants exhibited a synchronous hind limb locomotion defect or "hopping gait" phenotype, which is also characteristic of EphA4 null mice. Genetic complementation experiments suggested that Epha4(rb-2J) corresponds to an allele of EphA4, but details of the genomic defect in this mouse mutant are currently unavailable. We found a single base-pair deletion in exon 9 resulting in a frame shift mutation that subsequently resulted in a premature stop codon. Analysis of the predicted structure of the truncated protein suggests that both the kinase and sterile α motif (SAM) domains are absent. Definitive determination of genotype is needed for experimental studies of mice carrying the Epha4(rb-2J) allele, and we have also developed a method to ease detection of the mutation through RFLP. Eph-ephrin family members are reportedly expressed as numerous isoforms. Hence, delineation of the specific mutation in EphA4 in this strain is important for further functional studies, such as protein-protein interactions, immunostaining and gene compensatory studies, investigating the mechanism underlying the effects of altered function of Eph family of receptor tyrosine kinases on phenotype.

Matched MeSH terms: Codon, Terminator