Simple sequence is abundant in eukaryotic proteins

Gb, Golding

doi:10.1110/ps.8.6.1358

Cited by 45 publications

(37 citation statements)

References 29 publications

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“…The latter organism was chosen for its similarity to P. berghei in the A + T content of coding regions. The results, reported in the last two columns of Table 1, indicate that in both cases hydrophilic low-complexity regions exhibit a strong preference for the polar residues asparagine, serine, and glutamine and a less-marked preference for threonine, proline, and glutamic acid, in agreement with reports analyzing, respectively, simple segments common to different proteins (Golding 1999) and homopeptide repeats (Mar-Albà et al 1999) in S. cerevisiae.…”

Section: Genome Research 221supporting

confidence: 88%

“…The yeast choice (Ser, Asn, Gln, Asp, Thr, and Pro, in order of decreasing excess frequency with respect to complex regions) confirms previous data on low-complexity motifs shared by different yeast proteins (Golding 1999). The amino acid choice in D. discoideum closely resembles that of yeast.…”

Section: Genome Research 225supporting

confidence: 85%

“…For S. cerevisiae, amino acid preferences in homopolymeric tracts and the distribution of these tracts among different classes of proteins are described by Mar Albà et al (1999). Simple segments common to many yeast proteins have been characterized by Golding (1999) and shown to contain preferentially Ser, Asn, Gln, Asp, Glu, and Thr residues. The investigator observed that no particular feature justifies this amino acid choice, which is poorly suited to the formation of useful secondary or tertiary structures.…”

Section: Discussionmentioning

confidence: 99%

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Low-Complexity Regions in Plasmodium falciparum Proteins

Pizzi¹

2001

Genome Research

113

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Section: Genome Research 221supporting

confidence: 88%

Section: Genome Research 225supporting

confidence: 85%

Section: Discussionmentioning

confidence: 99%

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Low-Complexity Regions in Plasmodium falciparum Proteins

Pizzi¹

2001

Genome Research

113

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“…In addition to the putative chloroplast signal peptide, Motif Scan identified several stretches of low-complexity regions (29). These regions exhibit little diversity regarding their amino acid composition and are common in many eukaryotic proteins (39)(40)(41). Raa8 carries an alanine-rich region that covers nearly the entire protein, in addition to serine-, glycine-, glutamine-, and proline-rich stretches (Fig.…”

Section: Resultsmentioning

confidence: 99%

The Octatricopeptide Repeat Protein Raa8 Is Required for Chloroplast trans Splicing

2015

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The mRNA maturation of the tripartite chloroplast psaA gene from the green alga Chlamydomonas reinhardtii depends on various nucleus-encoded factors that participate in trans splicing of two group II introns. Recently, a multiprotein complex was identified that is involved in processing the psaA precursor mRNA. Using coupled tandem affinity purification (TAP) and mass spectrometry analyses with the trans-splicing factor Raa4 as a bait protein, we recently identified a multisubunit ribonucleoprotein (RNP) complex comprising the previously characterized trans-splicing factors Raa1, Raa3, Raa4, and Rat2 plus novel components. Raa1 and Rat2 share a structural motif, an octatricopeptide repeat (OPR), that presumably functions as an RNA interaction module. Two of the novel RNP complex components also exhibit a predicted OPR motif and were therefore considered potential trans-splicing factors. In this study, we selected bacterial artificial chromosome (BAC) clones encoding these OPR proteins and conducted functional complementation assays using previously generated trans-splicing mutants. Our assay revealed that the trans-splicing defect of mutant F19 was restored by a new factor we named RAA8; molecular characterization of complemented strains verified that Raa8 participates in splicing of the first psaA group II intron. Three of six OPR motifs are located in the C-terminal end of Raa8, which was shown to be essential for restoring psaA mRNA trans splicing. Our results support the important role played by OPR proteins in chloroplast RNA metabolism and also demonstrate that combining TAP and mass spectrometry with functional complementation studies represents a vigorous tool for identifying trans-splicing factors. Interaction modules are crucial for the molecular and cellular function of proteins, and a wide repertoire of diverse domains and motifs mediates a variety of regulatory mechanisms. Proteins that exhibit a repeating structural unit with an ␣-helical architecture are classified as members of the ␣-solenoid superfamily (1). This large family is widely distributed in eukaryotes and includes, among others, the transcription activator-like (TAL) effectors, the tetratricopeptide repeat (TPR) proteins, and the pentatricopeptide repeat (PPR) proteins (2-4). The ␣-helical structure of diverse members mediates binding to either proteins or nucleic acids.A well-characterized example of RNA binding proteins is the PPR protein family (5). The degenerate PPR motif is described as two antiparallel, ␣-helical tracts of 35 amino acids, whose repeats are often arranged in tandem arrays. Recently, two approaches provided insights into the predictable RNA binding code of this motif (6, 7). Structural analyses indicate that RNA binding is mediated by helical tracts forming a superhelical groove with exposed residues. Despite the low sequence conservation of the PPR motif being restricted to several amino acids, PPR proteins specifically recognize single-stranded RNA sequences through a combinatorial amino acid code (2, 6, 7). Mod...

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“…One of the most commonly shared features between proteins in eukaryotic genomes is the abundance of simple sequences, characterized by low information content due to amino acid compositional bias (Golding 1999;Huntley and Golding 2000). Simple sequence composition varies from stretches of a single amino acid (hereafter homopolymer sequences) to repeats of a few residues.…”

mentioning

confidence: 99%

Genome-wide evidence for selection acting on single amino acid repeats

Haerty¹,

Golding²

2010

Genome Res.

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Low complexity and homopolymer sequences within coding regions are known to evolve rapidly. While their expansion may be deleterious, there is increasing evidence for a functional role associated with these amino acid sequences. Homopolymer sequences are thought to evolve mostly through replication slippage and, therefore, they may be expected to be longer in regions with relaxed selective constraint. Within the coding sequences of eukaryotes, alternatively spliced exons are known to evolve under relaxed constraints in comparison to those exons that are constitutively spliced because they are not included in all of the mature mRNA of a gene. This relaxed exposure to selection leads to faster rates of evolution for alternatively spliced exons in comparison to constitutively spliced exons. Here, we have tested the effect of splicing on the structure (composition, length) of homopolymer sequences in relation to the splicing pattern in which they are found. We observed a significant relationship between alternative splicing and homopolymer sequences with alternatively spliced genes being enriched in number and length of homopolymer sequences. We also observed lower codon diversity and longer homocodons, suggesting a balance between slippage and point mutations linked to the constraints imposed by selection.

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Simple sequence is abundant in eukaryotic proteins

Cited by 45 publications

References 29 publications

Low-Complexity Regions in Plasmodium falciparum Proteins

Low-Complexity Regions in Plasmodium falciparum Proteins

The Octatricopeptide Repeat Protein Raa8 Is Required for Chloroplast trans Splicing

Genome-wide evidence for selection acting on single amino acid repeats

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