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Radó-Trilla N, Albà M. Dissecting the role of low-complexity regions in the evolution of vertebrate proteins. BMC Evol Biol 2012; 12:155. [PMID: 22920595 PMCID: PMC3523016 DOI: 10.1186/1471-2148-12-155] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 07/30/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few amino acids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly contribute to increase protein sequence space and generate novel protein functions. However, little is known about the global impact of LCRs on protein evolution. RESULTS We have traced back the evolutionary history of 2,802 LCRs from a large set of homologous protein families from H.sapiens, M.musculus, G.gallus, D.rerio and C.intestinalis. Transcriptional factors and other regulatory functions are overrepresented in proteins containing LCRs. We have found that the gain of novel LCRs is frequently associated with repeat expansion whereas the loss of LCRs is more often due to accumulation of amino acid substitutions as opposed to deletions. This dichotomy results in net protein sequence gain over time. We have detected a significant increase in the rate of accumulation of novel LCRs in the ancestral Amniota and mammalian branches, and a reduction in the chicken branch. Alanine and/or glycine-rich LCRs are overrepresented in recently emerged LCR sets from all branches, suggesting that their expansion is better tolerated than for other LCR types. LCRs enriched in positively charged amino acids show the contrary pattern, indicating an important effect of purifying selection in their maintenance. CONCLUSION We have performed the first large-scale study on the evolutionary dynamics of LCRs in protein families. The study has shown that the composition of an LCR is an important determinant of its evolutionary pattern.
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Affiliation(s)
- Núria Radó-Trilla
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics - IMIM Hospital del Mar Research Institute, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona 08003, Spain
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Toll-Riera M, Radó-Trilla N, Martys F, Albà MM. Role of low-complexity sequences in the formation of novel protein coding sequences. Mol Biol Evol 2011; 29:883-6. [PMID: 22045997 DOI: 10.1093/molbev/msr263] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Low-complexity sequences are extremely abundant in eukaryotic proteins for reasons that remain unclear. One hypothesis is that they contribute to the formation of novel coding sequences, facilitating the generation of novel protein functions. Here, we test this hypothesis by examining the content of low-complexity sequences in proteins of different age. We show that recently emerged proteins contain more low-complexity sequences than older proteins and that these sequences often form functional domains. These data are consistent with the idea that low-complexity sequences may play a key role in the emergence of novel genes.
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Affiliation(s)
- Macarena Toll-Riera
- Evolutionary Genomics Group, Research Programme in Biomedical Informatics, Universitat Pompeu Fabra (UPF)-Institute Municipal d'Investigació Mèdica (IMIM), Barcelona, Spain
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Zhang L, Yu S, Cao Y, Wang J, Zuo K, Qin J, Tang K. Distributional gradient of amino acid repeats in plant proteins. Genome 2007; 49:900-5. [PMID: 17036065 DOI: 10.1139/g06-054] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A computer-based analysis was conducted to assess the characteristics of amino acid repeats in Arabidopsis and rice. Our analysis showed a negative gradient in amino acid repeat distribution along the direction of translation in plants. Repeat occurrences are obviously associated with position in plant proteins but are not consistent with the corresponding amino acid contents. These repeats are encoded by the mixed synonymous codons rather than the uninterrupted reiterations of a single codon, and both Arabidopsis and rice have gradients in their distribution. Functional investigation showed that these repeat-containing proteins are preferentially involved in transcription regulation and protein ubiquitination but significantly underrepresented in the processes of DNA recombination and DNA replication. These data reveal that the direction-related mutation bias and functional selection have influenced the distribution of amino acid repeats in plants.
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Affiliation(s)
- Lida Zhang
- Plant Biotechnology Research Center, Institute of Systems Biology, Shanghai Key Laboratory of Agrobiotechnology, Fudan-SJTU-Nottingham Plant Biotechnology R & D Center, School of Agriculture, Shanghai, China
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Bonomi G. Long stretches of sequential and identical serine or alanine codons are compatible with an efficient full-length protein expression in Escherichia coli. Protein Expr Purif 2006; 48:160-6. [PMID: 16600623 DOI: 10.1016/j.pep.2006.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 02/15/2006] [Accepted: 02/15/2006] [Indexed: 11/26/2022]
Abstract
The Schistosoma japonicum glutathione S-transferase (GST) recombinant cDNAs, carrying blocks of sequential and identical triplets, consisting of 15-30-45 GCT (Ala) codons or 15-30 and also up to 75 AGC (Ser) codons, are expressed efficiently in an Escherichia coli system in the form of full-length protein chains, as detected by Coomassie-stained SDS-polyacrylamide gels, and soluble fusion proteins are purified by GSH-affinity chromatography. High expression levels and high yields of purified recombinant proteins are achieved. The efficient protein expression is independent of the molecular context and position of the polySer/polyAla string inserted into the GST carrier (near the part of the gene encoding the N- or the C-terminus). These findings suggest that E. coli is a powerful biological system to express foreign genes carrying long stretches coding for Ser- or Ala-rich domains, which are not uncommon in eukaryotic proteins. Moreover, data reported here show that the negative effect of sequential serine codons on protein expression in bacteria, previously reported in the literature, is not a general phenomenon.
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Affiliation(s)
- Giovanna Bonomi
- Institute of Genetics and Biophysics Adriano Buzzati - Traverso, CNR, Naples, Italy.
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Abstract
Amino acid tandem repeats, also called homopolymeric tracts, are extremely abundant in eukaryotic proteins. To gain insight into the genome-wide evolution of these regions in mammals, we analyzed the repeat content in a large data set of rat-mouse-human orthologs. Our results show that human proteins contain more amino acid repeats than rodent proteins and that trinucleotide repeats are also more abundant in human coding sequences. Using the human species as an outgroup, we were able to address differences in repeat loss and repeat gain in the rat and mouse lineages. In this data set, mouse proteins contain substantially more repeats than rat proteins, which can be at least partly attributed to a higher repeat loss in the rat lineage. The data are consistent with a role for trinucleotide slippage in the generation of novel amino acid repeats. We confirm the previously observed functional bias of proteins with repeats, with overrepresentation of transcription factors and DNA-binding proteins. We show that genes encoding amino acid repeats tend to have an unusually high GC content, and that differences in coding GC content among orthologs are directly related to the presence/absence of repeats. We propose that the different GC content isochore structure in rodents and humans may result in an increased amino acid repeat prevalence in the human lineage.
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Affiliation(s)
- M Mar Albà
- Grup de Recerca en Informàtica Biomèdica, Departament de Ciències Experimentals i de la Salut, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, 08003 Barcelona, Spain.
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Abstract
Protein simple sequences are a subclass of low complexity regions of sequence that are highly enriched in one or a few residue types. Such sequences are common in transcription regulatory proteins, in structural proteins, in proteins involved in nucleic acid interactions, and in mediating protein-protein interactions. Simple sequences of 10 or more residues, containing >/=50% of a single residue type are surveyed in this work. Both eukaryote and prokaryote proteomes are investigated with emphasis on the eukaryotes. Very large numbers of such sequences are found in all organisms surveyed. It is found that eukaryotes possess far more simple sequences per protein than do the prokaryotes. Prokaryotes display a linear relationship between number of proteins containing simple sequences and proteome size, whereas it is not clear that such a relationship holds for eukaryotes. Strikingly, it is found that each eukaryote possesses its own unique distribution of simple sequences. Within those distributions it is found that simple sequences enriched in certain residue types are clearly favored, whereas others are just as clearly discriminated against. The preferences observed are not correlated with residue occurrence. An analysis of classes of proteins of known function suggests that simple sequence occurrence and distribution may be related to protein function. Based upon this analysis, the large number of simple sequences found above that would be expected from a simple statistical model, plus the known functional importance of numerous such sequences, it is postulated that eukaryotes have evolved to not only tolerate large numbers of simple sequences but also to require them.
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Affiliation(s)
- Kim Lan Sim
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536-0298, USA
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Abstract
Tandem repeats in GenBank primate nucleotide sequences annotated as protein coding regions are analyzed. It is found that only trinucleotide repeats show repeat enrichment well above the threshold of statistical significance. The statistics are improved by a simultaneous search for repeats on both the amino acid and nucleotide levels. The results of the analyses of natural sequences are interpreted by comparing them with the results of the computer simulation of the model dedicated to protein coding regions. According to the simulation results, a limited set of trinucleotides, that is, cgg, ccg, cag, and gaa repeats coding for polyalanine, polyglycine, polyproline, polyglutamine, and polylysine are prone to proliferation. It is also found that within the repeat regions slippage is more frequent by a factor of 10 than point mutations, whereas the ratio of silent versus recognizable point mutations is approximately the same as elsewhere in coding regions. The trinucleotide repeats cover slightly more than 0.3% of the protein coding regions of genes.
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Affiliation(s)
- Branko Borstnik
- National Institute of Chemistry, SI-1001 Ljubljana, Slovenia.
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Abstract
Amino acids interact with each other, especially with neighboring amino acids, to generate protein structures. We studied the pattern of association and repulsion of amino acids based on 24,748 protein-coding genes from human, 11,321 from mouse, and 15,028 from Escherichia coli, and documented the pattern of neighbor preference of amino acids. All amino acids have different preferences for neighbors. We have also analyzed 7,342 proteins with known secondary structure and estimated the propensity of the 20 amino acids occurring in three of the major secondary structures, i.e., helices, sheets, and turns. Much of the neighbor preference can be explained by the propensity of the amino acids in forming different secondary structures, but there are also a number of intriguing association and repulsion patterns. The similarity in neighbor preference among amino acids is significantly correlated with the number of amino acid substitutions in both mitochondrial and nuclear genes, with amino acids having similar sets of neighbors replacing each other more frequently than those having very different sets of neighbors. This similarity in neighbor preference is incorporated into a new index of amino acid dissimilarities that can predict nonsynonymous codon substitutions better than the two existing indices of amino acid dissimilarities, i.e., Grantham's and Miyata's distances.
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Affiliation(s)
- Xuhua Xia
- Bioinformatics Laboratory, HKU-Pasteur Research Center, Dexter H.C. Man Building, 8 Sassoon Road, Pokfulam, Hong Kong.
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Hancock JM, Worthey EA, Santibáñez-Koref MF. A Role for Selection in Regulating the Evolutionary Emergence of Disease-Causing and Other Coding CAG Repeats in Humans and Mice. Mol Biol Evol 2001; 18:1014-23. [PMID: 11371590 DOI: 10.1093/oxfordjournals.molbev.a003873] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The evolutionary expansion of CAG repeats in human triplet expansion disease genes is intriguing because of their deleterious phenotype. In the past, this expansion has been suggested to reflect a broad genomewide expansion of repeats, which would imply that mutational and evolutionary processes acting on repeats differ between species. Here, we tested this hypothesis by analyzing repeat- and flanking-sequence evolution in 28 repeat-containing genes that had been sequenced in humans and mice and by considering overall lengths and distributions of CAG repeats in the two species. We found no evidence that these repeats were longer in humans than in mice. We also found no evidence for preferential accumulation of CAG repeats in the human genome relative to mice from an analysis of the lengths of repeats identified in sequence databases. We then investigated whether sequence properties, such as base and amino acid composition and base substitution rates, showed any relationship to repeat evolution. We found that repeat-containing genes were enriched in certain amino acids, presumably as the result of selection, but that this did not reflect underlying biases in base composition. We also found that regions near repeats showed higher nonsynonymous substitution rates than the remainder of the gene and lower nonsynonymous rates in genes that contained a repeat in both the human and the mouse. Higher rates of nonsynonymous mutation in the neighborhood of repeats presumably reflect weaker purifying selection acting in these regions of the proteins, while the very low rate of nonsynonymous mutation in proteins containing a CAG repeat in both species presumably reflects a high level of purifying selection. Based on these observations, we propose that the mutational processes giving rise to polyglutamine repeats in human and murine proteins do not differ. Instead, we propose that the evolution of polyglutamine repeats in proteins results from an interplay between mutational processes and selection.
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Affiliation(s)
- J M Hancock
- MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, London, England.
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Nishizawa M, Nishizawa K. Amino acid and nucleotide recurrence in aligned sequences: synonymous substitution patterns in association with global and local base compositions. Nucleic Acids Res 2000; 28:3801-10. [PMID: 11000273 PMCID: PMC110763 DOI: 10.1093/nar/28.19.3801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The tendency for repetitiveness of nucleotides in DNA sequences has been reported for a variety of organisms. We show that the tendency for repetitive use of amino acids is widespread and is observed even for segments conserved between human and Drosophila melanogaster at the level of >50% amino acid identity. This indicates that repetitiveness influences not only the weakly constrained segments but also those sequence segments conserved among phyla. Not only glutamine (Q) but also many of the 20 amino acids show a comparable level of repetitiveness. Repetitiveness in bases at codon position 3 is stronger for human than for D.melanogaster, whereas local repetitiveness in intron sequences is similar between the two organisms. While genes for immune system-specific proteins, but not ancient human genes (i.e. human homologs of Escherichia coli genes), have repetitiveness at codon bases 1 and 2, repetitiveness at codon base 3 for these groups is similar, suggesting that the human genome has at least two mechanisms generating local repetitiveness. Neither amino acid nor nucleotide repetitiveness is observed beyond the exon boundary, denying the possibility that such repetitiveness could mainly stem from natural selection on mRNA or protein sequences. Analyses of mammalian sequence alignments show that while the 'between gene' GC content heterogeneity, which is linked to 'isochores', is a principal factor associated with the bias in substitution patterns in human, 'within gene' heterogeneity in nucleotide composition is also associated with such bias on a more local scale. The relationship amongst the various types of repetitiveness is discussed.
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Affiliation(s)
- M Nishizawa
- Department of Biochemistry, Teikyo University School of Medicine, Kaga, Itabashi, Tokyo 173, Japan
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