scholarly journals Evolution of the highly repetitive PEVK region of titin across mammals

2018 ◽  
Author(s):  
Kathleen Muenzen ◽  
Jenna Monroy ◽  
Findley R. Finseth
Keyword(s):  
Mammalian Species ◽  
Raw Material ◽  
Actin Binding ◽  
Evolutionary Constraint ◽  
Length Variation ◽  
Evolutionary Adaptation ◽  
Model Species ◽  
Vertebrate Muscle ◽  
Alternatively Spliced ◽  
Pevk Region

ABSTRACTThe protein titin plays a key role in vertebrate muscle where it acts like a giant molecular spring. Despite its importance and conservation over vertebrate evolution, a lack of high quality annotations in non-model species makes comparative evolutionary studies of titin challenging. The PEVK region of titin—named for its high proportion of Pro-Glu-Val-Lys amino acids—is particularly difficult to annotate due to its abundance of alternatively spliced isoforms and short, highly repetitive exons. To understand PEVK evolution across mammals, we first developed a bioinformatics tool, PEVK_Finder, to annotate PEVK exons from genomic sequences of titin and then applied it to a diverse set of mammals. PEVK_Finder consistently outperforms standard annotation tools across a broad range of conditions and improves annotations of the PEVK region in non-model mammalian species. We find that the PEVK region can be divided into two subregions (PEVK-N, PEVK-C) with distinct patterns of evolutionary constraint and divergence. The bipartite nature of the PEVK region has implications for titin diversification. In the PEVK-N region, certain exons are conserved and may be essential, but natural selection also acts on particular codons. This region is also rich in glutamate and may contribute to actin binding. In the PEVK-C, exons are more homogenous and length variation of the PEVK region may provide the raw material for evolutionary adaptation in titin function. Taken together, we find that the very complexity that makes titin a challenge for annotation tools may also promote evolutionary adaptation.

Evolutionary adaptation of a mammalian species to an environment severely depleted of iodide

2003 ◽  
Vol 446 (1) ◽  
pp. 42-45 ◽  
Author(s):  
Gertrudis Cabello ◽  
Arnaldo Vilaxa ◽  
Angel E. Spotorno ◽  
John Valladares ◽  
Mark Pickard ◽  
...  
Keyword(s):  
Mammalian Species ◽  
Evolutionary Adaptation

scholarly journals Alternatively spliced exons of the beta tropomyosin gene exhibit different affinities for F-actin and effects with nonmuscle caldesmon

1995 ◽  
Vol 108 (10) ◽  
pp. 3253-3265 ◽  
Author(s):  
M.F. Pittenger ◽  
A. Kistler ◽  
D.M. Helfman
Keyword(s):  
Skeletal Muscle ◽  
Smooth Muscle ◽  
Insect Cell ◽  
The Other ◽  
Actin Binding ◽  
Gene Products ◽  
Free Concentration ◽  
Alternatively Spliced ◽  
Beta Gene

The rat beta-tropomyosin (TM) gene expresses two isoforms via alternative RNA splicing, namely skeletal muscle beta-TM and fibroblast TM-1. The latter is also expressed in smooth muscle where it corresponds to smooth muscle beta-TM. Skeletal muscle beta-TM contains exons 7 and 10, whereas exons 6 and 11 are used in fibroblasts and smooth muscle. In order to study the properties of the alternatively spliced proteins, recombinant TMs derived from bacterial and insect cell expression systems were produced, including the normal beta gene products, fibroblast TM-1 and beta skeletal muscle TM, two carboxy-terminal chimeric TMs, TM-6/10 and TM-7/11, as well as a carboxyl-truncated version of each, TM-6Cla and TM-7Cla. The purified TM isoforms were used in actin filament association studies. The apparent TM association constants (Ka) were taken as the free concentration at half saturation and were found to be 6 microM for beta Sk TM, 8.5 for TM-6/10, 25 microM for TM-1, and 30 microM for TM-7/11 at an F-actin concentration of 42 microM. For the truncated TMs, the values determined were higher still but the binding was not carried out to full saturation. Isoforms were also produced using the baculovirus-insect cell system which produces proteins with an acetylated amino terminus as is normally found in vivo. This modification significantly enhanced the F-actin association of TM-1 but not the beta skeletal TM or the other isoforms. Fibroblast TM-2 or TM-3, both products of the alpha gene, enhanced the affinity of TM-1 for F-actin, demonstrating different isoforms can act cooperatively on binding to actin. This effect was not detected with the other expressed beta gene products. The presence of 83 kDa nonmuscle caldesmon was found to enhance the binding of TM-1 for F-actin. This effect was dependent on the presence of both exons 6 and 11, as caldesmon had little effect on the other beta gene products. Collectively these results demonstrate TMs differ in their affinity for F-actin, which can be altered by other TMs or actin-binding proteins. The beta tropomyosin isoforms were fluorescently-tagged and microinjected into cultured cells to study their in vivo localization where it was found that each of the full-length TMs bound to microfilaments but, at the light microscopy level, the isoforms were not differentially localized in these fibroblasts.

Variations in apparent mass of mammalian fast-type myosin light chains correlate with species body size, from shrew to elephant

2007 ◽  
Vol 292 (1) ◽  
pp. R527-R534 ◽  
Author(s):  
Sabahattin Bicer ◽  
Peter J. Reiser
Keyword(s):  
Molecular Weight ◽  
Body Mass ◽  
Mammalian Species ◽  
Actin Binding ◽  
Light Chains ◽  
Myosin Light Chains ◽  
Low Molecular Weight ◽  
Myofibrillar Proteins ◽  
Strongly Correlated ◽  
Electrophoretic Mobilities

A recent study (Bicer S and Reiser PJ. J Muscle Res Cell Motil 25: 623–633, 2004) suggested considerable variation in the apparent molecular mass (Ma), deduced from electrophoretic mobility, in fast-type myosin light chains (MLCF), especially MLC1F, among mammalian species. Furthermore, there was an indication that MLC1F Ma generally correlates with species body mass, over an ∼4,000-fold range in body mass. The results also suggested that Ma of other low-molecular-weight myofibrillar proteins is less variable and not as strongly correlated with body mass among the same species. The objective of this study was to test the hypotheses that the Ma of MLCs does, in fact, vary and correlate with species body mass. The electrophoretic mobilities of MLCF isoforms from 19 species, varying in size ∼500,000-fold, were quantitated. The results confirm that the Ma of MLC1F and MLC2F vary significantly among mammals, spanning a very broad range in body mass; the MLC1F Ma varies more than that of other low-molecular-weight myofibrillar proteins; and there is a significant correlation between species body mass and MLC1F Ma. Differences in MLC1F Ma among five species can be accounted for by differences in the reported amino acid sequence, especially the length of a common polyalanine region near the NH2-terminal actin-binding site. The possibility that the differences in MLC1F sequence among mammalian species, in and adjacent to the actin-binding region, are related to differences in modulation of cross-bridge kinetics in species with diverse locomotion kinetics is discussed.

scholarly journals The Role of Co-Deleted Genes in Neurofibromatosis Type 1 Microdeletions: An Evolutive Approach

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 839
Author(s):  
Larissa Brussa Reis ◽  
Andreia Carina Turchetto-Zolet ◽  
Maievi Fonini ◽  
Patricia Ashton-Prolla ◽  
Clévia Rosset
Keyword(s):  
Positive Selection ◽  
Neurofibromatosis Type 1 ◽  
Mammalian Species ◽  
Ring Finger ◽  
Purifying Selection ◽  
Neurofibromatosis Type ◽  
Evolutionary Constraint ◽  
Loss Of Function ◽  
Cancer Predisposition Syndrome

Neurofibromatosis type 1 (NF1) is a cancer predisposition syndrome that results from dominant loss-of-function mutations mainly in the NF1 gene. Large rearrangements are present in 5–10% of affected patients, generally encompass NF1 neighboring genes, and are correlated with a more severe NF1 phenotype. Evident genotype–phenotype correlations and the importance of the co-deleted genes are difficult to establish. In our study we employed an evolutionary approach to provide further insights into the understanding of the fundamental function of genes that are co-deleted in subjects with NF1 microdeletions. Our goal was to access the ortholog and paralog relationship of these genes in primates and verify if purifying or positive selection are acting on these genes. Fourteen genes were analyzed in twelve mammalian species. Of these, four and ten genes showed positive selection and purifying selection, respectively. The protein, RNF135, showed three sites under positive selection at the RING finger domain, which may have been selected to increase efficiency in ubiquitination routes in primates. The phylogenetic analysis suggests distinct evolutionary constraint between the analyzed genes. With these analyses, we hope to help clarify the correlation of the co-deletion of these genes and the more severe phenotype of NF1.

Physical and genetic interaction of filamin with presenilin in Drosophila

2000 ◽  
Vol 113 (19) ◽  
pp. 3499-3508 ◽  
Author(s):  
Y. Guo ◽  
S.X. Zhang ◽  
N. Sokol ◽  
L. Cooley ◽  
G.L. Boulianne
Keyword(s):  
Transmembrane Domain ◽  
Genetic Interaction ◽  
Amino Acid Identity ◽  
Binding Domain ◽  
Actin Binding ◽  
Loop Region ◽  
Actin Binding Domain ◽  
Alternatively Spliced ◽  
The Central Nervous System ◽  
Hydrophilic Loop

Presenilins were first identified as causative factors in early onset, familial Alzheimer's Disease (FAD). They are predicted to encode a highly conserved novel family of eight transmembrane domain proteins with a large hydrophilic loop between TM6 and TM7 that is the site of numerous FAD mutations. Here, we show that the loop region of Drosophila and human presenilins interacts with the C-terminal domain of Drosophila filamin. Furthermore, we show that Drosophila has at least two major filamin forms generated by alternative splicing from a gene that maps to position 89E10-89F4 on chromosome 3. The longest form is enriched in the central nervous system and ovaries, shares 41.7% overall amino acid identity with human filamin (ABP-280) and contains an N-terminal actin-binding domain. The shorter form is broadly expressed and encodes an alternatively spliced form of the protein lacking the actin-binding domain. Finally, we show that presenilin and filamin are expressed in overlapping patterns in Drosophila and that dominant adult phenotypes produced by overexpression of presenilin can be suppressed by overexpression of filamin in the same tissue. Taken together, these results suggest that presenilin and filamin functionally interact during development.

scholarly journals Forced expression of chimeric human fibroblast tropomyosin mutants affects cytokinesis.

1995 ◽  
Vol 129 (3) ◽  
pp. 697-708 ◽  
Author(s):  
K S Warren ◽  
J L Lin ◽  
J P McDermott ◽  
J J Lin
Keyword(s):  
Cho Cells ◽  
Actin Filaments ◽  
Human Fibroblasts ◽  
Fine Tuning ◽  
Actin Binding ◽  
Functional Consequences ◽  
Alternatively Spliced ◽  
Carboxy Terminal

Human fibroblasts generate at least eight tropomyosin (TM) isoforms (hTM1, hTM2, hTM3, hTM4, hTM5, hTM5a, hTM5b, and hTMsm alpha) from four distinct genes, and we have previously demonstrated that bacterially produced chimera hTM5/3 exhibits an unusually high affinity for actin filaments and a loss of the salt dependence typical for TM-actin binding (Novy, R.E., J. R. Sellers, L.-F. Liu, and J.J.-C. Lin, 1993. Cell Motil. & Cytoskeleton. 26: 248-261). To examine the functional consequences of expressing this mutant TM isoform in vivo, we have transfected CHO cells with the full-length cDNA for hTM5/3 and compared them to cells transfected with hTM3 and hTM5. Immunofluorescence microscopy reveals that stably transfected CHO cells incorporate force-expressed hTM3 and hTM5 into stress fibers with no significant effect on general cell morphology, microfilament organization or cytokinesis. In stable lines expressing hTM5/3, however, cell division is slow and sometimes incomplete. The doubling time and the incidence of multinucleate cells in the stable hTM5/3 lines roughly parallel expression levels. A closely related chimeric isoform hTM5/2, which differs only in the internal, alternatively spliced exon also produces defects in cytokinesis, suggesting that normal TM function may involve coordination between the amino and carboxy terminal regions. This coordination may be prevented in the chimeric mutants. As bacterially produced hTM5/3 and hTM5/2 can displace hTM3 and hTM5 from actin filaments in vitro, it is likely that CHO-expressed hTM5/3 and hTM5/2 can displace endogenous TMs to act dominantly in vivo. These results support a role for nonmuscle TM isoforms in the fine tuning of microfilament organization during cytokinesis. Additionally, we find that overexpression of TM does not stabilize endogenous microfilaments, rather, the hTM-expressing cells are actually more sensitive to cytochalasin B. This suggests that regulation of microfilament integrity in vivo requires stabilizing factors other than, or in addition to, TM.

scholarly journals Titin Diversity—Alternative Splicing Gone Wild

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Wei Guo ◽  
Sheila J. Bharmal ◽  
Karla Esbona ◽  
Marion L. Greaser
Keyword(s):  
Alternative Splicing ◽  
Single Individual ◽  
Large Protein ◽  
Vast Number ◽  
Splicing Pattern ◽  
Specific Manner ◽  
Alternatively Spliced ◽  
Isoform Expression ◽  
Pevk Region ◽  
Human Heart Disease

Titin is an extremely large protein found in highest concentrations in heart and skeletal muscle. The single mammalian gene is expressed in multiple isoforms as a result of alternative splicing. Although titin isoform expression is controlled developmentally and in a tissue specific manner, the vast number of potential splicing pathways far exceeds those described in any other alternatively spliced gene. Over 1 million human splice pathways for a single individual can be potentially derived from the PEVK region alone. A new splicing pattern for the human cardiac N2BA isoform type has been found in which the PEVK region includes only the N2B type exons. The alterations in splicing and titin isoform expression in human heart disease provide impetus for future detailed study of the splicing mechanisms for this giant protein.

Looking into a whale’s heart: investigating a genetic basis for cardiomyopathy in a non-model species

Genome ◽  
2017 ◽  
Vol 60 (8) ◽  
pp. 695-705
Author(s):  
Amélia Viricel ◽  
Patricia E. Rosel
Keyword(s):  
Mammalian Species ◽  
Mutation Screening ◽  
Sperm Whale ◽  
Muscle Disease ◽  
Control Group ◽  
Incomplete Penetrance ◽  
Model Species ◽  
Cetacean Species ◽  
Deep Diving ◽  
Age Related

Understanding the pathogenesis of complex diseases can benefit from multi-species comparative studies. Yet these studies rarely include natural populations of non-model species. Here, we focused on the cause of a heart muscle disease, cardiomyopathy (CM), affecting multiple mammalian species including humans, cats, dogs, and certain species of whales. Mutations in genes coding for sarcomeric proteins have been identified as a leading cause for CM in humans, and some were also revealed to be responsible for CM in cats. We investigated whether similar mutations could be detected in the deep-diving pygmy sperm whale (Kogia breviceps), which is one of two cetacean species known to display CM. We sequenced portions of two candidate genes (MYH7: 3153 bp and MYBPC3: 3019 bp) in 55 whales including affected and unaffected individuals. Mutation screening revealed six nonsynonymous substitutions that were predicted to have an effect on protein function. However, the etiology of CM is likely complex and probably multi-factorial as three of these mutations were observed in unaffected individuals from our control group. This incomplete penetrance could be partly age-related and could also be due to the influence of environmental factors on the development of CM, as seen in humans.

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