Displaying publications 1 - 20 of 80 in total

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  1. Monajemi H, Daud MN, Mohd Zain S, Wan Abdullah WA
    Biochem. Cell Biol., 2012 Dec;90(6):691-700.
    PMID: 23016605 DOI: 10.1139/o2012-027
    Finding a proper transition structure for the peptide bond formation process can lead one to a better understanding of the role of ribosome in catalyzing this reaction. Using computer simulations, we performed the potential energy surface scan on the ester bond dissociation of P-site aminoacyl-tRNA and the peptide bond formation of P-site and A-site amino acids. The full fragments of initiator tRNA(i)(met) and elongator tRNA(phe) are attached to both cognate and non-cognate amino acids as the P-site substrate. The A-site amino acid for all four calculations is methionine. We used ONIOM calculations to reduce the computational cost. Our study illustrates the reduced rate of peptide bond formation for misacylated tRNA(i)(met) in the absence of ribosomal bases. The misacylated elongator tRNA(phe), however, did not show any difference in its PES compared with that for the phe-tRNA(phe). This demonstrates the structural specification of initiator tRNA(i)(met) for the amino acids side chain.
    Matched MeSH terms: RNA, Transfer, Amino Acyl/metabolism; RNA, Transfer, Met/metabolism; RNA, Transfer, Met/chemistry*; RNA, Transfer, Phe/metabolism; RNA, Transfer, Phe/chemistry*
  2. Monajemi H, M Zain S, Wan Abdullah WAT
    PMID: 34047250 DOI: 10.1080/15257770.2021.1923742
    The translational accuracy in protein synthesis is contributed to by several mechanisms in the ribosome, generally called kinetic proofreading. This process in the ribosome inhibits the non-cognate codon-anticodon interaction. However, it is not sufficient for fidelity of protein synthesis since a wrong amino acid can easily be added to the growing polypeptide chain if a tRNA while cognate to the mRNA, carries a non-cognate amino acid. Therefore, additional to the kinetic proofreading, there must be some hitherto unknown characteristic in misacylated-tRNAs to stop the process of protein synthesis if such misacylated-tRNA is accommodated in the ribosomal A-site. In order to understand this characteristic, we have performed computational quantum chemistry analysis on five different tRNA molecules, each one attached to five different amino acids with one being cognate to the tRNA and the other four non-cognate. This study shows the importance of aminoacyl-tRNA binding energy in ensuring fidelity of protein synthesis.
    Matched MeSH terms: RNA, Transfer*
  3. Monajemia, H., Daud, M.N., Zain, S.M., Wan Abdullah, W.A.T.
    ASM Science Journal, 2012;6(2):138-143.
    MyJurnal
    Finding a proper transition structure for the peptide bond formation process can lead to a better understanding of the role of the ribosome in catalyzing this reaction. A potential energy surface scan was performed on the ester bond dissociation of the P-site aminoacyl-tRNA and the peptide bond formation of P-site and A-site amino acids. The full fragment of initiator tRNAi met attached to both cognate (met) and non-cognate (ala) amino acids as the P-site substrate and the methionine as the A-site amino acid was used in this study. Due to the large size of tRNA, ONIOM calculations were used to reduce the computational cost. This study illustrated that the rate of peptide bond formation was reduced for misacylated tRNA without the presence of ribosomal bases. This demonstrated that there were indeed specific structural interactions involving the amino acid side chain within the tRNAi met.
    Matched MeSH terms: RNA, Transfer; RNA, Transfer, Amino Acyl
  4. Monajemi H, Omar NY, Daud MN, Zain SM, Abdullah WA
    PMID: 21902474 DOI: 10.1080/15257770.2011.605780
    The proper arrangement of amino acids in a protein determines its proper function, which is vital for the cellular metabolism. This indicates that the process of peptide bond formation requires high fidelity. One of the most important processes for this fidelity is kinetic proofreading. As biochemical experiments suggest that kinetic proofreading plays a major role in ensuring the fidelity of protein synthesis, it is not certain whether or not a misacylated tRNA would be corrected by kinetic proofreading during the peptide bond formation. Using 2-layered ONIOM (QM/MM) computational calculations, we studied the behavior of misacylated tRNAs and compared the results with these for cognate aminoacyl-tRNAs during the process of peptide bond formation to investigate the effect of nonnative amino acids on tRNAs. The difference between the behavior of initiator tRNA(i) (met) compared to the one for the elongator tRNAs indicates that only the initiator tRNA(i) (met) specifies the amino acid side chain.
    Matched MeSH terms: RNA, Transfer/metabolism; RNA, Transfer/chemistry; RNA, Transfer, Met/metabolism; RNA, Transfer, Met/chemistry*
  5. Kaewdaungdee S, Sudmoon R, Tanee T, Lee SY, Chaveerach A
    Genes (Basel), 2022 Sep 22;13(10).
    PMID: 36292590 DOI: 10.3390/genes13101705
    In order to authenticate the genomic information of Barleriacristata L., B. lupulina Lindl., B. repens Nees, B. siamensis Craib, and B. strigosa Willd, cp genomes were investigated. They revealed a general structure with a total size of 151,997-152,324 bp. The genomes encoded a total of 131 genes, including 86 CDS, 37 tRNA, and 8 rRNA genes. Other details found were as follows: different numbers and types of SSRs; identical gene content, which is adjacent to the border regions, except for B. strigosa, that revealed a shorter ndhF gene sequence and lacked the ycf1 gene; slightly different genetic distance values, which can be used for species identification; three distinct gaps of nucleotide variations between the species located at the intergenic spacer regions of the LSC and CDS of the SSC; three effective molecular markers derived from divergent hotspot regions, including the ccsA-ndhD, ndhA-ndhH-rps15, and ycf1. The genetic relationships derived from the cp genome and the CDS phylogenetic trees of Barleria and the 13 genera in Acanthaceae and different families, Scrophulariaceae and Phrymaceae, showed similar results. The six Barleria species as monophyletic groups with inner and outer outgroups were found to have perfect discrimination. These results have helped to authenticate the five Barleria species and the six genera in Acanthaceae.
    Matched MeSH terms: RNA, Transfer/genetics
  6. Soo OYM, Gastineau R, Verdon G, Winsor L, Justine JL
    Zootaxa, 2023 May 03;5277(3):585-599.
    PMID: 37518300 DOI: 10.11646/zootaxa.5277.3.11
    We present here the first observation of Bipalium admarginatum de Beauchamp, 1933 since its original description 90 years ago. Three specimens were found on Perhentian Kecil Island, off Terengganu State, Malaysia and photographed in the field, and two were collected. This report thus includes the first colour photographs published for this species, from a locality close to the type-locality, Tioman Island (which is ca. 200 km south of the locality in this study, on the east coast of Peninsula Malaysia). We describe the external morphology and colour pattern of the species, which correspond well to the original description, itself based only on two preserved specimens. We performed an in-depth molecular characterisation of the species, including its complete mitochondrial genome, the 18S sequence and elongation 1-alpha (EF1-α) sequence. In addition, EF1-α sequences were also retrieved for 5 additional geoplanid species. No tRNA-Thr could be detected in the mitogenome of B. admarginatum, a lack already reported in several species of geoplanids, but we found a 13 bp sequence that contains the anticodon loop and seems to be conserved among geoplanids and might thus possibly represent a non-canonical undetected tRNA. We discuss the difficulties encountered in trying to reconstruct the cluster of nuclear ribosomal genes, a problem already mentioned for other Triclads. Three phylogenies, based respectively on all mitochondrial proteins, 18S, and EF1-α, were computed; the position of B. admarginatum within the Bipaliinae was confirmed in each tree, as sister-group to various bipaliine species according to the sequences available for each tree. In the mitochondrial proteins tree, which had high support, B. admarginatum was sister to Bipalium kewense and Diversibipalium multilineatum.
    Matched MeSH terms: RNA, Transfer/genetics
  7. Wakamiya T, Tingek S, Okuyama H, Kiyoshi T, Takahashi JI
    Mitochondrial DNA B Resour, 2017 Jan 17;2(1):24-25.
    PMID: 33490434 DOI: 10.1080/23802359.2016.1275847
    In this study, we analyzed the complete mitochondrial genome of the cavity-nesting honeybee, A. koschevnikovi. The mitochondrial genome of A. koschevnikovi was observed to be a circular molecule of 15,278 bp and was similar to that of the other cavity-nesting honeybee species. The average AT content in the A. koschevnikovi mitochondrial genome was 84%. It was predicted to contain 13 protein-coding, 24 tRNA and two rRNA genes, along with one A + T-rich control region, besides three tRNA-Met repeats.
    Matched MeSH terms: RNA, Transfer
  8. Yoon KB, Kim JY, Park YC
    PMID: 25418628 DOI: 10.3109/19401736.2014.982571
    We describe the characteristics of complete mitogenome of C. brachyotis in this article. The complete mitogenome of C. brachyotis is 16,701 bp long with a total base composition of 32.4% A, 25.7% T, 27.7% C and 14.2% G. The mitogenome consists of 13 protein-coding genes (11,408 bp), (KM659865) two rRNA (12S rRNA and 16S rRNA) genes (2,539 bp), 22 tRNA genes (1518 bp) and one control region (1239 bp).
    Matched MeSH terms: RNA, Transfer/genetics
  9. Tan MH, Gan HM, Lee YP, Austin CM
    PMID: 25423512 DOI: 10.3109/19401736.2014.982587
    The mitochondrial genome sequence of the ghost crab, Ocypode ceratophthalmus, is documented (GenBank accession number: LN611669) in this article. This is the first mitogenome for the family Ocypodidae and the second for the order Ocypodoidea. Ocypode ceratophthalmus has a mitogenome of 15,564 base pairs consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the O. ceratophthalmus mitogenome is 35.78% for T, 19.36% for C, 33.73% for A and 11.13% for G, with an AT bias of 69.51% and the gene order is the typical arrangement for brachyuran crabs.
    Matched MeSH terms: RNA, Transfer/genetics
  10. Tan MH, Gan HM, Lee YP, Austin CM
    PMID: 25423510 DOI: 10.3109/19401736.2014.982585
    The Mictyris longicarpus (soldier crab) complete mitochondrial genome sequence is reported making it the first for the family Mictyridae and the second for the superfamily Ocypodoidea. The mitogenome is 15,548 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The soldier crab mitogenome gene order is characteristic of brachyuran crabs with a base composition of 36.58% for T, 19.15% for C, 32.43% for A and 11.83% for G, with an AT bias of 69.01%.
    Matched MeSH terms: RNA, Transfer/genetics
  11. Gan HM, Tan MH, Gan HY, Lee YP, Austin CM
    PMID: 25648918 DOI: 10.3109/19401736.2015.1007325
    The clawed lobster Nephrops norvegicus is an important commercial species in European waters. We have sequenced the complete mitochondrial genome of the species from a partial genome scan using Next-Gen sequencing. The N. norvegicus has a mitogenome of 16,132 base pairs (71.22% A+ T content) comprising 13 protein-coding genes, 2 ribosomal subunit genes, 21 transfer RNAs, and a putative 1259 bp non-coding AT-rich region. This mitogenome is the second fully characterized for the family Nephropidae and the first for the genus Nephrops. The mitogenome gene order is identical to the Maine lobster, Homarus americanus with the exception of the possible loss of the trnI gene.
    Matched MeSH terms: RNA, Transfer/genetics
  12. Gan HY, Gan HM, Lee YP, Austin CM
    PMID: 25693708 DOI: 10.3109/19401736.2015.1007311
    The mitochondrial genome of the rock pool prawn (Palaemon serenus), is sequenced, making it the third for genera of the family Palaemonidae and the first for the genus Palaemon. The mitogenome is 15,967 base pairs in length and comprises 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The P. serenus mitogenome has an AT bias of 58.97% and a base composition of 29.79% for T, 24.14% for C, 29.18% for A, and 16.89% for G. The mitogenome gene order of P. serenus is identical to Exopalaemon carinicauda.
    Matched MeSH terms: RNA, Transfer/genetics
  13. Gan HY, Gan HM, Lee YP, Austin CM
    PMID: 25693707 DOI: 10.3109/19401736.2015.1007312
    The mitochondrial genome sequence of the Australian freshwater shrimp, Paratya australiensis, is presented, which is the fourth for genera of the superfamily Atyoidea and the first atyid from the southern hemisphere. The base composition of the P. australiensis, mitogenome is 33.55% for T, 18.24% for C, 35.16% for A, and 13.06% for G, with an AT bias of 71.58%. It has a mitogenome of 15,990 base pairs comprised of 13 protein-coding, 2 ribosomal subunit and 22 transfer RNAs genes and a non-coding AT-rich region. The mitogenome gene order for the species is typical for atyid shrimps, which conform to the primitive pan crustacean model.
    Matched MeSH terms: RNA, Transfer/genetics
  14. Austin CM, Tan MH, Croft LJ, Meekan MG, Gan HY, Gan HM
    PMID: 25693694 DOI: 10.3109/19401736.2015.1007348
    The complete mitogenome of the ray Taeniura lymma was recovered from genome skimming using the HiSeq sequencing system. The T. lymma mitogenome has 17,652 base pairs (59.13% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a 1906 bp non-coding AT-rich region. This mitogenome sequence is the second for a ray from Australian waters, the first for the genus Taeniura and the ninth for the family Dasyatidae.
    Matched MeSH terms: RNA, Transfer/genetics
  15. Gan HM, Tan MH, Lee YP, Hammer MP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4187-4188.
    PMID: 25600740
    The mitogenome of an Australian sample of the mudskipper, Periophthalmus minutus, was recovered from partial sequencing using the MiSeq sequencer. This mudskipper has a mitogenome of 16,506 base pairs (55% A + T content) made up of two ribosomal subunit genes, 13 protein-coding genes, 22 transfer RNAs, and a 838 bp non-coding AT-rich region. This is the first sequenced mitogenome for the genus Periophthalmus and the fifth for the subfamily Oxudercinae.
    Matched MeSH terms: RNA, Transfer/genetics*
  16. Austin CM, Tan MH, Lee YP, Croft LJ, Meekan MG, Gan HM
    PMID: 25103432 DOI: 10.3109/19401736.2014.947586
    The complete mitogenome of the ray Pastinachus atrus was recovered from a partial genome scan using the HiSeq sequencing system. The P. atrus mitogenome has 18,162 base pairs (61% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 2516 bp non-coding AT-rich region. This mitogenome sequence is the first for a ray from Australian waters, the first for the Genus Pastinachus, and the 6th for the family Dasyatidae.
    Matched MeSH terms: RNA, Transfer/genetics
  17. Gan HM, Tan MH, Thai BT, Austin CM
    PMID: 24617474 DOI: 10.3109/19401736.2014.892104
    The complete mitochondrial genome of the commercially important snout otter clam Lutraria rhynchaena was obtained from low-coverage shotgun sequencing data on the MiSeq platform. The L. rhynchaena mitogenome has 16,927 base pairs (69% A + T content) and made up of 12 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 953 bp non-coding AT-rich region. This is the first mitogenome to be sequenced from the genus Lutraria, and the seventh to be reported for the family Mactridae.
    Matched MeSH terms: RNA, Transfer/genetics
  18. Ho CL, Lee WK, Lim EL
    Genomics, 2018 03;110(2):124-133.
    PMID: 28890206 DOI: 10.1016/j.ygeno.2017.09.003
    Agar and agarose have wide applications in food and pharmaceutical industries. Knowledge on the genome of red seaweeds that produce them is still lacking. To fill the gap in genome analyses of these red algae, we have sequenced the nuclear and organellar genomes of an agarophyte, Gracilaria changii. The partial nuclear genome sequence of G. changii has a total length of 35.8Mb with 10,912 predicted protein coding sequences. Only 39.4% predicted proteins were found to have significant matches to protein sequences in SwissProt. The chloroplast genome of G. changii is 183,855bp with a total of 201 open reading frames (ORFs), 29 tRNAs and 3 rRNAs predicted. Five genes: ssrA, leuC and leuD CP76_p173 (orf139) and pbsA were absent in the chloroplast genome of G. changii. The genome information is valuable in accelerating functional studies of individual genes and resolving evolutionary relationship of red seaweeds.
    Matched MeSH terms: RNA, Transfer/genetics
  19. Grismer LL, Muin MA, Wood PL, Anuar S, Linkem CW
    Zootaxa, 2016 Mar 15;4092(2):231-42.
    PMID: 27394452 DOI: 10.11646/zootaxa.4092.2.6
    Phylogenetic analyses based on the mitochondrial gene ND2 and its flanking tRNAs indicate the diminutive upland and insular species Sphenomorphus bukitensis, S. butleri, S. langkawiensis, S. perhentianensis, and S. temengorensis form a monophyletic group that is phylogenetically embedded within the Southeast Asian genus Tytthoscincus. The analyses also indicate that a new swamp-dwelling skink from the Bukit Panchor State Park, Pulau Pinang, Peninsular Malaysia is the sister species to the swamp-dwelling species S. sibuensis from Pulau Sibu, Johor and Singapore and that these two are also embedded in the genus Tytthoscincus. By transferring the two Peninsular Malaysian clades of Sphenomorphus into the genus Tytthoscincus, the monophyly of the latter is maintained. The new species T. panchorensis sp. nov. can be distinguished from all other species of Tytthoscincus by having a unique combination of morphological and color pattern characteristics.
    Matched MeSH terms: RNA, Transfer/genetics*
  20. Lee SY, Ng WL, Hishamuddin MS, Mohamed R
    Mitochondrial DNA B Resour, 2019;4(1):19-20.
    PMID: 33365402 DOI: 10.1080/23802359.2018.1535848
    Known for its durable timber quality, Neobalanocarpus heimii (King) Ashton is a highly sought after tree species endemic to the Malay Peninsula. Due to its scarcity and high value, the tree is classified under the IUCN Red List categories of Vulnerable. In this study, we assembled the complete chloroplast (cp) genome of N. heimii using data from high-throughput Illumina sequencing. The Chengal cp genome is 151,191 bp in size and includes two inverted repeat regions of 23,721 bp each, which is separated by a large single copy region of 83,801 bp and a small single copy region of 19,948 bp. A total of 130 genes were predicted, including 37 tRNA, 8 rRNA, and 85 protein-coding genes. Phylogenetic analysis placed N. heimii within the order Malvales.
    Matched MeSH terms: RNA, Transfer
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