Evolution of the isoelectric point of mammalian proteins as a consequence of indels and adaptive evolution

Alendé, Nicolas; Shields, Denis C.; Khaldi, Nora

doi:10.1002/prot.22990

Cited by 13 publications

(11 citation statements)

References 39 publications

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“…Both sequence length and selection have been recently shown to explain the observed differences in pI between mammalian orthologs [5]. We argue that the differences in the digestive systems due to pH and compartmentalization of the different mammals is not the sole driver of major changes in pI , and that these selective changes might be due to functional divergence of the protein.…”

Section: Introductionmentioning

confidence: 74%

Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species

Khaldi

Shields

2011

Biology Direct

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BackgroundMilk proteins are required to proceed through a variety of conditions of radically varying pH, which are not identical across mammalian digestive systems. We wished to investigate if the shifts in these requirements have resulted in marked changes in the isoelectric point and charge of milk proteins during evolution.ResultsWe investigated nine major milk proteins in 13 mammals. In comparison with a group of orthologous non-milk proteins, we found that 3 proteins κ-casein, lactadherin, and muc1 have undergone the highest change in isoelectric point during evolution. The pattern of non-synonymous substitutions indicate that selection has played a role in the isoelectric point shift, since residues that show significant evidence of positive selection are much more likely to be charged (p = 0.03 for κ-casein; p < 10-8 for muc1). However, this selection does not appear to be solely due to adaptation to the diversity of mammalian digestive systems, since striking changes are seen among species that resemble each other in terms of their digestion.ConclusionThe changes in charge are most likely due to changes of other protein functions, rather than an adaptation to the different mammalian digestive systems. These functions may include differences in bioactive peptide releases in the gut between different mammals, which are known to be a major contributing factor in the functional and nutritional value of mammalian milk. This raises the question of whether bovine milk is optimal in terms of particular protein functions, for human nutrition and possibly disease resistance.This article was reviewed by Fyodor Kondrashov, David Liberles (nominated by David Ardell), and Christophe Lefevre (nominated by Mark Ragan).

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Section: Introductionmentioning

confidence: 74%

Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species

Khaldi

Shields

2011

Biology Direct

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“…In Eukaryotes, changes in the protein isoelectric point (iP) may directly influence the localization and reactions of proteins, and it is reasonable to assume that alterations to the global protein iP may interfere in interactions between proteins and complexes. Alendé et al [29], studying the evolution of iP over mammalian proteins, showed that insertions/deletions were the main reason for the shift in iP and suggested that shifts in iP might be related to the gain in additional activities, such as new interacting partners or preferences for orthologous or isoforms.…”

Section: Resultsmentioning

confidence: 99%

De novo transcriptome analysis of Hevea brasiliensistissues by RNA-seq and screening for molecular markers

Salgado¹,

Koop

Pinheiro³

et al. 2014

BMC Genomics

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BackgroundThe rubber tree, Hevea brasiliensis, is a species native to the Brazilian Amazon region and it supplies almost all the world’s natural rubber, a strategic raw material for a variety of products. One of the major challenges for developing rubber tree plantations is adapting the plant to biotic and abiotic stress. Transcriptome analysis is one of the main approaches for identifying the complete set of active genes in a cell or tissue for a specific developmental stage or physiological condition.ResultsHere, we report on the sequencing, assembling, annotation and screening for molecular markers from a pool of H. brasiliensis tissues. A total of 17,166 contigs were successfully annotated. Then, 2,191 Single Nucleotide Variation (SNV) and 1.397 Simple Sequence Repeat (SSR) loci were discriminated from the sequences. From 306 putative, mainly non-synonymous SNVs located in CDS sequences, 191 were checked for their ability to characterize 23 Hevea genotypes by an allele-specific amplification technology. For 172 (90%), the nucleotide variation at the predicted genomic location was confirmed, thus validating the different steps from sequencing to the in silico detection of the SNVs.ConclusionsThis is the first study of the H. brasiliensis transcriptome, covering a wide range of tissues and organs, leading to the production of the first developed SNP markers. This process could be amplified to a larger set of in silico detected SNVs in expressed genes in order to increase the marker density in available and future genetic maps. The results obtained in this study will contribute to the H. brasiliensis genetic breeding program focused on improving of disease resistance and latex yield.

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“…SPDIR can generate near-random genetic variations and alter entire protein domains in a single generation. It is thus tempting to speculate that SPDIR may be an important mechanism in protein evolution (42) following gene amplification and duplication events (43) (Supporting Information).…”

Section: Discussionmentioning

confidence: 99%

Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms

Harms

Lunnan

Hülter

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome.

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Evolution of the isoelectric point of mammalian proteins as a consequence of indels and adaptive evolution

Cited by 13 publications

References 39 publications

Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species

Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species

De novo transcriptome analysis of Hevea brasiliensistissues by RNA-seq and screening for molecular markers

Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms

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