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Glidden-Handgis G, Wheeler TJ. WAS IT A MATch I SAW? Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences. BIOINFORMATICS ADVANCES 2024; 4:vbae052. [PMID: 38764475 PMCID: PMC11099658 DOI: 10.1093/bioadv/vbae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 03/31/2024] [Accepted: 04/04/2024] [Indexed: 05/21/2024]
Abstract
Background Software for labeling biological sequences typically produces a theory-based statistic for each match (the E-value) that indicates the likelihood of seeing that match's score by chance. E-values accurately predict false match rate for comparisons of random (shuffled) sequences, and thus provide a reasoned mechanism for setting score thresholds that enable high sensitivity with low expected false match rate. This threshold-setting strategy is challenged by real biological sequences, which contain regions of local repetition and low sequence complexity that cause excess matches between non-homologous sequences. Knowing this, tool developers often develop benchmarks that use realistic-seeming decoy sequences to explore empirical tradeoffs between sensitivity and false match rate. A recent trend has been to employ reversed biological sequences as realistic decoys, because these preserve the distribution of letters and the existence of local repeats, while disrupting the original sequence's functional properties. However, we and others have observed that sequences appear to produce high scoring alignments to their reversals with surprising frequency, leading to overstatement of false match risk that may negatively affect downstream analysis. Results We demonstrate that an alignment between a sequence S and its (possibly mutated) reversal tends to produce higher scores than alignment between truly unrelated sequences, even when S is a shuffled string with no notable repetitive or low-complexity regions. This phenomenon is due to the unintuitive fact that (even randomly shuffled) sequences contain palindromes that are on average longer than the longest common substrings (LCS) shared between permuted variants of the same sequence. Though the expected palindrome length is only slightly larger than the expected LCS, the distribution of alignment scores involving reversed sequences is strongly right-shifted, leading to greatly increased frequency of high-scoring alignments to reversed sequences. Impact Overestimates of false match risk can motivate unnecessarily high score thresholds, leading to potentially reduced true match sensitivity. Also, when tool sensitivity is only reported up to the score of the first matched decoy sequence, a large decoy set consisting of reversed sequences can obscure sensitivity differences between tools. As a result of these observations, we advise that reversed biological sequences be used as decoys only when care is taken to remove positive matches in the original (un-reversed) sequences, or when overstatement of false labeling is not a concern. Though the primary focus of the analysis is on sequence annotation, we also demonstrate that the prevalence of internal palindromes may lead to an overstatement of the rate of false labels in protein identification with mass spectrometry.
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Affiliation(s)
| | - Travis J Wheeler
- R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ 85721, United States
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2
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Xiong N, Xie D, Dong Y, Xue YP, Zheng YG. Efficient biosynthesis of 1-cyanocyclohexaneacetic acid using a highly soluble nitrilase by N-terminus modification of novel peptide tags. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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3
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An IL13Rα2 peptide exhibits therapeutic activity against metastatic colorectal cancer. Br J Cancer 2018; 119:940-949. [PMID: 30318506 PMCID: PMC6203792 DOI: 10.1038/s41416-018-0259-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/07/2018] [Accepted: 08/16/2018] [Indexed: 12/28/2022] Open
Abstract
Background Interleukin 13 receptor α2 (IL13Rα2) is overexpressed in metastatic colorectal cancer. Here, we have developed novel strategies to block IL-13 binding to IL13Rα2 in order to reduce metastatic spread. Methods Synthetic IL13Rα2 D1 peptide (GSETWKTIITKN) was tested for the inhibition of IL-13 binding to IL13Rα2 using ELISA and different cellular assays. Peptide blocking effects on different cell signalling mediators were determined by western blot. An enantiomer version of the peptide (D-D1) was prepared to avoid proteolytic digestion. Nude mice were used for tumour growth and survival analysis after treatment with IL13Rα2 peptides. Results IL13Rα2 D1 peptide inhibited migration, invasion, and proliferation in metastatic colorectal and glioblastoma cancer cells treated with IL-13. Residues 82K, 83T, 85I and 86T were essential for blocking IL-13. IL13Rα2 peptide abolished ligand-mediated receptor internalisation and degradation, and substantially decreased IL-13 signalling capacity through IL13Rα2 to activate the FAK, PI3K/AKT and Src pathways as well as MT1-MMP expression. In addition, D1 significantly inhibited IL-13-mediated STAT6 activation through IL13Rα1. Nude mice treated with the enantiomer D-D1 peptide showed a remarkable survival increase. Conclusions We propose that the D-D1 peptide from IL13Rα2 represents a promising therapeutic agent to inhibit metastatic progression in colorectal cancer and, likely, other solid tumours.
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Kaya N, Alsagob M, D'Adamo MC, Al-Bakheet A, Hasan S, Muccioli M, Almutairi FB, Almass R, Aldosary M, Monies D, Mustafa OM, Alyounes B, Kenana R, Al-Zahrani J, Naim E, Binhumaid FS, Qari A, Almutairi F, Meyer B, Plageman TF, Pessia M, Colak D, Al-Owain M. KCNA4 deficiency leads to a syndrome of abnormal striatum, congenital cataract and intellectual disability. J Med Genet 2016; 53:786-792. [PMID: 27582084 DOI: 10.1136/jmedgenet-2015-103637] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 07/20/2016] [Accepted: 08/06/2016] [Indexed: 12/24/2022]
Abstract
BACKGROUND Voltage-gated potassium channels are highly diverse proteins representing the most complex class of voltage-gated ion channels from structural and functional perspectives. Deficiency of these channels usually results in various human disorders. OBJECTIVES To describe a novel autosomal recessive syndrome associated with KCNA4 deficiency leading to congenital cataract, abnormal striatum, intellectual disability and attention deficit hyperactivity disorder. METHODS We used SNP arrays, linkage analyses, autozygosity mapping, whole-exome sequencing, RT-PCR and two-electrode voltage-clamp recording. RESULTS We identified a missense variant (p.Arg89Gln) in KCNA4 in four patients from a consanguineous family manifesting a novel syndrome of congenital cataract, abnormal striatum, intellectual disability and attention deficit hyperactivity disorder. The variant was fully segregated with the disease and absent in 747 ethnically matched exomes. Xenopus oocytes were injected with human Kv1.4 wild-type mRNA, R89Q and WT/R89Q channels. The wild type had mean current amplitude that was significantly greater than those recorded from the cells expressing the same amount of mutant mRNA. Co-expression of the wild type and mutant mRNAs resulted in mean current amplitude that was significantly different from that of the wild type. RT-PCR indicated that KCNA4 is present in mouse brain, lens and retina. KCNA4 interacts with several molecules including synaptotagmin I, DLG1 and DLG2. The channel co-localises with cholinergic amacrine and rod bipolar cells in rats and is widely distributed in the central nervous system. Based on previous studies, the channel is highly expressed in outer retina, rod inner segments, hippocampus and concentrated in axonal membranes. CONCLUSION KCNA4 (Kv1.4) is implicated in a novel syndrome characterised by striatal thinning, congenital cataract and attention deficit hyperactivity disorder. Our study highlights potassium channels' role in ocular and neuronal genetics.
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Affiliation(s)
- Namik Kaya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Maysoon Alsagob
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Maria Cristina D'Adamo
- Section of Physiology and Biochemistry, Department of Experimental Medicine, University of Perugia School of Medicine, Perugia, Italy
| | - Albandary Al-Bakheet
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sonia Hasan
- Section of Physiology and Biochemistry, Department of Experimental Medicine, University of Perugia School of Medicine, Perugia, Italy
| | - Maria Muccioli
- College of Optometry, The Ohio State University, Columbus, Ohio, USA
| | - Faten B Almutairi
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Rawan Almass
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mazhor Aldosary
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Osama M Mustafa
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Banan Alyounes
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Rosan Kenana
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Jawaher Al-Zahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Eva Naim
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Faisal S Binhumaid
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Alya Qari
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fatema Almutairi
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Brian Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | | | - Mauro Pessia
- Section of Physiology and Biochemistry, Department of Experimental Medicine, University of Perugia School of Medicine, Perugia, Italy.,Department of Physiology & Biochemistry Faculty of Medicine & Surgery, University of Malta, Msida, Malta
| | - Dilek Colak
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- College of Optometry, The Ohio State University, Columbus, Ohio, USA.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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Migliolo L, Felício MR, Cardoso MH, Silva ON, Xavier MAE, Nolasco DO, de Oliveira AS, Roca-Subira I, Vila Estape J, Teixeira LD, Freitas SM, Otero-Gonzalez AJ, Gonçalves S, Santos NC, Franco OL. Structural and functional evaluation of the palindromic alanine-rich antimicrobial peptide Pa -MAP2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1488-98. [DOI: 10.1016/j.bbamem.2016.04.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/22/2016] [Accepted: 04/05/2016] [Indexed: 11/26/2022]
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6
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Sridhar S, Nagamruta M, Guruprasad K. Analyses of the Sequence and Structural Properties Corresponding to Pentapeptide and Large Palindromes in Proteins. PLoS One 2015; 10:e0139568. [PMID: 26465610 PMCID: PMC4605511 DOI: 10.1371/journal.pone.0139568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/15/2015] [Indexed: 11/18/2022] Open
Abstract
The analyses of 3967 representative proteins selected from the Protein Data Bank revealed the presence of 2803 pentapeptide and large palindrome sequences with known secondary structure conformation. These represent 2014 unique palindrome sequences. 60% palindromes are not associated with any regular secondary structure and 28% are in helix conformation, 11% in strand conformation and 1% in the coil conformation. The average solvent accessibility values are in the range between 0–155.28 Å2 suggesting that the palindromes in proteins can be either buried, exposed to the solvent or share an intermittent property. The number of residue neighborhood contacts defined by interactions ≤ 3.2 Ǻ is in the range between 0–29 residues. Palindromes of the same length in helix, strand and coil conformation are associated with different amino acid residue preferences at the individual positions. Nearly, 20% palindromes interact with catalytic/active site residues, ligand or metal ions in proteins and may therefore be important for function in the corresponding protein. The average hydrophobicity values for the pentapeptide and large palindromes range between -4.3 to +4.32 and the number of palindromes is almost equally distributed between the negative and positive hydrophobicity values. The palindromes represent 107 different protein families and the hydrolases, transferases, oxidoreductases and lyases contain relatively large number of palindromes.
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Affiliation(s)
- Settu Sridhar
- Bioinformatics, Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
| | - Mallapragada Nagamruta
- Bioinformatics, Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
| | - Kunchur Guruprasad
- Bioinformatics, Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
- * E-mail:
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7
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Egorov VV, Lebedev DV, Shaldzhyan AA, Sirotkin AK, Gorshkov AN, Mirgorodskaya OA, Grudinina NA, Vasin AV, Shavlovsky MM. A conservative mutant of a proteolytic fragment produced during fibril formation enhances fibrillogenesis. Prion 2015; 8:369-73. [PMID: 25551549 DOI: 10.4161/19336896.2014.983745] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The fibrillogenesis of a peptide corresponding to residues 35-51 of human α-lactalbumin (¹GYDTQAIVENNESTEYG¹⁷) can be dramatically enhanced by the addition of a tetrapeptide TDYG homologous to its C-terminus (TEYG). Generation of spontaneous hydrolytic products similar to this peptide was demonstrated by mass-spectrometry analysis of GYDTQAIVENNESTEYG peptide solution components during fibrillogenesis. Possible mechanisms and roles of short peptides in protein metabolism are discussed.
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Affiliation(s)
- Vladimir V Egorov
- a FSBI Research Institute of Influenza; Ministry of Healthcare of the Russian Federation ; St. Petersburg , Russia
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8
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Silva LP, Rech EL. Unravelling the biodiversity of nanoscale signatures of spider silk fibres. Nat Commun 2014; 4:3014. [PMID: 24345771 DOI: 10.1038/ncomms4014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 11/26/2013] [Indexed: 11/09/2022] Open
Abstract
Living organisms are masters at designing outstanding self-assembled nanostructures through a hierarchical organization of modular proteins. Protein-based biopolymers improved and selected by the driving forces of molecular evolution are among the most impressive archetypes of nanomaterials. One of these biomacromolecules is the myriad of compound fibroins of spider silks, which combine surprisingly high tensile strength with great elasticity. However, no consensus on the nano-organization of spider silk fibres has been reached. Here we explore the biodiversity of spider silk fibres, focusing on nanoscale characterization with high-resolution atomic force microscopy. Our results reveal an evolution of the nanoroughness, nanostiffness, nanoviscoelastic, nanotribological and nanoelectric organization of microfibres, even when they share similar sizes and shapes. These features are related to unique aspects of their molecular structures. The results show that combined nanoscale analyses of spider silks may enable the screening of appropriate motifs for bioengineering synthetic fibres from recombinant proteins.
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Affiliation(s)
- Luciano P Silva
- Embrapa Genetic Resources and Biotechnology, PBI, Parque Estação Biológica Final W5 Norte, Brasilia 70770-917, Brazil
| | - Elibio L Rech
- Embrapa Genetic Resources and Biotechnology, PBI, Parque Estação Biológica Final W5 Norte, Brasilia 70770-917, Brazil
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Ahmed Z, Gurusaran M, Narayana P, Kumar KSD, Mohanapriya J, Vaishnavi MK, Sekar K. PPS: A computing engine to find Palindromes in all Protein sequences. Bioinformation 2014; 10:48-51. [PMID: 24516327 PMCID: PMC3916820 DOI: 10.6026/97320630010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 01/23/2014] [Accepted: 01/24/2014] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED The primary structure of a protein molecule comprises a linear chain of amino acid residues. Certain parts of this linear chain are unique in nature and function. They can be classified under different categories and their roles studied in detail. Two such unique categories are the palindromic sequences and the Single Amino Acid Repeats (SAARs), which plays a major role in the structure, function and evolution of the protein molecule. In spite of their presence in various protein sequences, palindromes have not yet been investigated in detail. Thus, to enable a comprehensive understanding of these sequences, a computing engine, PPS, has been developed. The users can search the occurrences of palindromes and SAARs in all the protein sequences available in various databases and can view the three-dimensional structures (in case it is available in the known three-dimensional protein structures deposited to the Protein Data Bank) using the graphics plug-in Jmol. The proposed server is the first of its kind and can be freely accessed through the World Wide Web. AVAILABILITY URL http://pranag.physics.iisc.ernet.in/pps/
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Affiliation(s)
- Zameer Ahmed
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India
| | - Manickam Gurusaran
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India
| | - Prasanth Narayana
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India
| | - Kala Sekar Dinesh Kumar
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India
| | - Jayapal Mohanapriya
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India
| | | | - Kanagaraj Sekar
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India
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Gurusaran M, Ravella D, Sekar K. RepEx: repeat extractor for biological sequences. Genomics 2013; 102:403-8. [PMID: 23880222 DOI: 10.1016/j.ygeno.2013.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 06/28/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
Genomic sequences are far from being random but are made up of systematically ordered and information rich patterns. These repeated sequence patterns have been vastly utilized for their fundamental importance in understanding the genome function and organization. To this end, a comprehensive toolkit, RepEx, has been developed which extracts repeat (inverted, everted and mirror) patterns from the given genome sequence(s) without any constraints. The toolkit can also be used to fetch the inverted repeats present in the protein sequence(s). Further, it is capable of extracting exact and degenerate repeats with a user defined spacer intervals. It is remarkably more precise and sensitive when compared to the existing tools. An example with comprehensive case studies and a performance evaluation of the proposed toolkit has been presented to authenticate its efficiency and accuracy.
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Affiliation(s)
- M Gurusaran
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India
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11
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Špoljarić D, Ugrina I. On Statistical Properties of Palindromes in DNA. COMMUN STAT-THEOR M 2013. [DOI: 10.1080/03610926.2012.739253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Prasanth N, Vaishnavi MK, Sekar K. An algorithm to find all palindromic sequences in proteins. J Biosci 2013; 38:173-7. [PMID: 23385825 DOI: 10.1007/s12038-013-9300-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A palindrome is a set of characters that reads the same forwards and backwards. Since the discovery of palindromic peptide sequences two decades ago, little effort has been made to understand its structural, functional and evolutionary significance. Therefore, in view of this, an algorithm has been developed to identify all perfect palindromes (excluding the palindromic subset and tandem repeats) in a single protein sequence. The proposed algorithm does not impose any restriction on the number of residues to be given in the input sequence. This avant-garde algorithm will aid in the identification of palindromic peptide sequences of varying lengths in a single protein sequence.
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Affiliation(s)
- N Prasanth
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012
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Du Y, Murani E, Ponsuksili S, Wimmers K. Flexible and efficient genome tiling design with penalized uniqueness score. BMC Bioinformatics 2012; 13:323. [PMID: 23216884 PMCID: PMC3583072 DOI: 10.1186/1471-2105-13-323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 10/26/2012] [Indexed: 11/24/2022] Open
Abstract
Background As a powerful tool in whole genome analysis, tiling array has been widely used in the answering of many genomic questions. Now it could also serve as a capture device for the library preparation in the popular high throughput sequencing experiments. Thus, a flexible and efficient tiling array design approach is still needed and could assist in various types and scales of transcriptomic experiment. Results In this paper, we address issues and challenges in designing probes suitable for tiling array applications and targeted sequencing. In particular, we define the penalized uniqueness score, which serves as a controlling criterion to eliminate potential cross-hybridization, and a flexible tiling array design pipeline. Unlike BLAST or simple suffix array based methods, computing and using our uniqueness measurement can be more efficient for large scale design and require less memory. The parameters provided could assist in various types of genomic tiling task. In addition, using both commercial array data and experiment data we show, unlike previously claimed, that palindromic sequence exhibiting relatively lower uniqueness. Conclusions Our proposed penalized uniqueness score could serve as a better indicator for cross hybridization with higher sensitivity and specificity, giving more control of expected array quality. The flexible tiling design algorithm incorporating the penalized uniqueness score was shown to give higher coverage and resolution. The package to calculate the penalized uniqueness score and the described probe selection algorithm are implemented as a Perl program, which is freely available at http://www1.fbn-dummerstorf.de/en/forschung/fbs/fb3/paper/2012-yang-1/OTAD.v1.1.tar.gz.
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Affiliation(s)
- Yang Du
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
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Analysis of compensatory substitution and gene evolution on the MAGEA/CSAG-palindrome of the primate X chromosomes. Comput Biol Chem 2012; 42:18-22. [PMID: 23257410 DOI: 10.1016/j.compbiolchem.2012.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 11/06/2012] [Accepted: 11/13/2012] [Indexed: 11/20/2022]
Abstract
The human X chromosome contains a large number of inverted repeat DNA palindromes. Although arbitrary substitutions destroyed the inverted repeat structure of MAGEA/CSAG-palindrome during the evolutionary process of the primates, most of the substitutions are compensatory. Using maximum parsimony, it is demonstrated that the compensatory substitutions are prone to occur between bases with similar structures on the human, chimpanzee and orangutan MAGEA/CSAG-palindromes. Furthermore, it is found that MAGEA/CSAG genes also exist in orangutan and rhesus monkey palindromes by homologous searching. This suggests that the MAGEA/CSAG-palindrome might predate the divergence of human and other primate lineages. Comparative sequence analysis of the arms and genes on the primate MAGEA/CSAG-palindromes provides possible evidence of subsequently arm to arm gene conversion. These compensatory substitutions on the MAGEA/CSAG-palindrome of the primate X chromosomes play an important role in maintaining their structural symmetry during the process of formation.
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The Effect of Sequence Complexity on the Construction of Protein-Protein Interaction Networks. Brain Inform 2010. [DOI: 10.1007/978-3-642-15314-3_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Qi YJ, Qiu WY. Symmetry Analysis of an X-palindrome in Human and Chimpanzee. CHINESE J CHEM PHYS 2009. [DOI: 10.1088/1674-0068/22/04/401-405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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