Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins

Proteins containing amino acid repeats are widespread among protozoan parasites. It has been suggested that these repetitive structures act as immunomodulators, but other functional aspects may be of primary importance. We have recently suggested that tandem repeats present in Trypanosoma cruzi trans-sialidase stabilize the catalytic activity in blood. Because the parasite releasestrans-sialidase, this delayed clearance of the enzyme might have implications in vivo. In the present work, the ability of repetitive units from different T. cruzi molecules in stabilizing trans-sialidase activity in blood was evaluated. It is shown that repeats present on T. cruzi shed proteins (antigens 13 and Shed-Acute-Phase-Antigen [SAPA]) increase trans-sialidase half-life in blood from 7 to almost 35 hours. Conversely, those repeats present in intracellular T. cruzi proteins only increase the enzyme half-life in blood up to 15 hours. Despite these results, comparative analysis of structural and catalytic properties of both groups of chimeric enzymes show no substantial differences. Interestingly, antigens 13 and SAPA also increase the persistence in blood of chimeric glutathione S-transferases, thus suggesting that this effect is inherent to these repeats and independent of the carrier protein. Although the molecular basis of this phenomenon is still uncertain, its biotechnological potential can be envisaged.

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Satellites in the prokaryote world

BMC Evolutionary Biology ◽

10.1186/s12862-019-1504-2 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Juan A. Subirana ◽

Xavier Messeguer

Keyword(s):

Amino Acid ◽

Tandem Repeats ◽

Reference Group ◽

Evolutionary Relationship ◽

Short Length ◽

Evolutionary Significance ◽

Leptospira Interrogans ◽

Amino Acid Repeats ◽

Representative Species ◽

Eukaryotic Genomes

Abstract Background Satellites or tandem repeats are very abundant in many eukaryotic genomes. Occasionally they have been reported to be present in some prokaryotes, but to our knowledge there is no general comparative study on their occurrence. For this reason we present here an overview of the distribution and properties of satellites in a set of representative species. Our results provide novel insights into the evolutionary relationship between eukaryotes, Archaea and Bacteria. Results We have searched all possible satellites present in the NCBI reference group of genomes in Archaea (142 species) and in Bacteria (119 species), detecting 2735 satellites in Archaea and 1067 in Bacteria. We have found that the distribution of satellites is very variable in different organisms. The archaeal Methanosarcina class stands out for the large amount of satellites in their genomes. Satellites from a few species have similar characteristics to those in eukaryotes, but most species have very few satellites: only 21 species in Archaea and 18 in Bacteria have more than 4 satellites/Mb. The distribution of satellites in these species is reminiscent of what is found in eukaryotes, but we find two significant differences: most satellites have a short length and many of them correspond to segments of genes coding for amino acid repeats. Transposition of non-coding satellites throughout the genome occurs rarely: only in the bacteria Leptospira interrogans and the archaea Methanocella conradii we have detected satellite families of transposed satellites with long repeats. Conclusions Our results demonstrate that the presence of satellites in the genome is not an exclusive feature of eukaryotes. We have described a few prokaryotes which do contain satellites. We present a discussion on their eventual evolutionary significance.

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Ribosome Evolution and Structural Capacitance

10.20944/preprints201908.0266.v1 ◽

2019 ◽

Author(s):

Ashley M Buckle ◽

Malcolm Buckle

Keyword(s):

Amino Acid ◽

Genetic Code ◽

Protein Evolution ◽

Bioinformatic Analysis ◽

Amino Acid Usage ◽

Loss Of Function ◽

Gain Of Function ◽

Acceptor Stem ◽

Ribosome Evolution ◽

Disordered Regions

In addition to the canonical loss-of-function mutations, mutations in proteins may additionally result in gain-of-function through the binary activation of cryptic ‘structural capacitance elements’. Our previous bioinformatic analysis allowed us to propose a new mechanism of protein evolution - structural capacitance – that arises via the generation of new elements of microstructure upon mutations that cause a disorder-to-order (DO) transition in previously disordered regions of proteins. Here we propose that the DO transition is a necessary follow-on from expected early codon-anticodon and tRNA acceptor stem-amino acid usage, via the accumulation of structural capacitance elements - reservoirs of disorder in proteins. We develop this argument further to posit that structural capacitance is an inherent consequence of the evolution of the genetic code.

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

Genome Research ◽

10.1101/gr.101246.109 ◽

2010 ◽

Vol 20 (6) ◽

pp. 755-760 ◽

Cited By ~ 23

Author(s):

W. Haerty ◽

G. B. Golding

Keyword(s):

Amino Acid ◽

Single Amino Acid ◽

Amino Acid Repeats ◽

Genome Wide

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Cross-reaction of antibodies to the nine-amino acid repeats ofPlasmodium falciparum antigen 11.1 with human serum albumin

European Journal of Immunology ◽

10.1002/eji.1830220214 ◽

1992 ◽

Vol 22 (2) ◽

pp. 381-385 ◽

Cited By ~ 4

Author(s):

Odile Mercereau-Puijalon ◽

Micheline Guillotte ◽

Noëlle Doyen

Keyword(s):

Amino Acid ◽

Human Serum Albumin ◽

Serum Albumin ◽

Human Serum ◽

Cross Reaction ◽

Amino Acid Repeats ◽

Ofplasmodium Falciparum

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The two major membrane skeletal proteins (articulins) of Euglena gracilis define a novel class of cytoskeletal proteins.

The Journal of Cell Biology ◽

10.1083/jcb.118.6.1465 ◽

1992 ◽

Vol 118 (6) ◽

pp. 1465-1475 ◽

Cited By ~ 45

Author(s):

J A Marrs ◽

G B Bouck

Keyword(s):

Amino Acid ◽

Fusion Protein ◽

Euglena Gracilis ◽

Cytoskeletal Proteins ◽

Cdna Clones ◽

Thin Sections ◽

Core Domain ◽

The Core ◽

Amino Acid Repeats ◽

Peptide Maps

60% of the peripheral membrane skeleton of Euglena gracilis consists of equimolar amounts of two proteins (articulins) with M(r)s in SDS gels of 80 and 86 kD. To understand eventually how these proteins assemble and function in maintaining cell form and membrane integrity we have undertaken a molecular characterization of articulins. A lambda gt11 expression library constructed from Euglena gracilis mRNAs was screened with antibodies against both articulins. Two sets of cDNAs were recovered, and evidence from three independent assays confirmed that both sets encoded articulins: (a) Anti-articulin antibodies recognized a high molecular weight beta-galactosidase (beta-gal) fusion protein expressed in bacteria infected with lambda gt11 cDNA clones. (b) Antibodies generated against the bacterially expressed beta-gal fusion protein identified one or the other articulin in Western blots of Euglena proteins. These antibodies also localized to the membrane skeletal region in thin sections of Euglena. (c) Peptide maps of the beta-gal fusion protein were similar to peptide maps of Euglena articulins. From the nucleotide sequence of the two sets of cDNAs an open reading frame for each articulin was deduced. In addition to 37% amino acid identity and overall structural similarity, both articulins exhibited a long core domain consisting of over 30 12-amino acid repeats with the consensus VPVPV--V--. Homology plots comparing the same or different articulins revealed larger, less regular repeats in the core domain that coincided with predicted turns in extended beta-sheets. Outside the core domain a short hydrophobic region containing four seven-amino acid repeats (consensus: APVTYGA) was identified near the carboxy terminus of the 80-kD articulin, but near the amino terminus of the 86-kD articulin. No extensive sequence similarities were found between articulins and other protein sequences in various databanks. We conclude that the two articulins are related members of a new class of membrane cytoskeletal proteins.

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