scholarly journals Analyses of the core eukaryotic protein subunit of telomerase support extensive adaptation to different evolutionary and life histories in the Metazoa

2016 ◽  
Author(s):  
Alvina G. Lai ◽  
Natalia Pouchkina-Stantcheva ◽  
Alessia Di Donfrancesco ◽  
Gerda Kildisiute ◽  
Sounak Sahu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Life Histories ◽  
Evolutionary History ◽  
Structural Evolution ◽  
Sequence Evolution ◽  
Dynamic Feature ◽  
Protein Subunit ◽  
Eukaryotic Protein ◽  
Telomere Biology ◽  
Splice Forms

AbstractMost animals employ telomerase, which consists of a catalytic subunit known as the telomerase reverse transcriptase (TERT) and an RNA template, to maintain telomere ends. Given the importance of TERT and the apparent importance of telomere biology in core metazoan life history traits like ageing and the control of somatic cell proliferation, we hypothesised that TERT would have patterns of sequence and regulatory evolution reflecting adaptations to diverse evolutionary and life histories across the Animal Kingdom. To test this, we performed a complete investigation of the evolutionary history of TERT across animals. We show that although TERT is almost ubiquitous across Metazoa, it has undergone substantial sequence evolution in canonical motifs. Beyond the known canonical motifs, we also identify and compare regions that are highly variable between lineages, but for which conservation exists within phyla. Recent data have highlighted the importance of alternate splice forms of TERT in non-canonical functions in some animals. Although animals may share some conserved introns, we find that the selection of exons for alternative splicing appears to be highly variable, and regulation by alternative splicing appears to be a very dynamic feature of TERT evolution. We show that even within a closely related group of triclad flatworms, where alternative splicing of TERT was previously correlated with reproductive strategy, we observe highly diverse alternative splicing patterns. Our work establishes that the evolutionary history and structural evolution of TERT involves previously unappreciated levels of change, supporting the view that this core eukaryotic protein has adapted to the requirements of diverse animal life histories.

scholarly journals Reconstructed protein sequence evolution consistent with the evolution of C4 photosynthesis via a C2 ancestor in the Paniceae

2019 ◽  
Author(s):  
Daniel S. Carvalho ◽  
Sunil Kumar Kenchanmane Raju ◽  
Yang Zhang ◽  
James C. Schnable
Keyword(s):  
Protein Sequence ◽  
Evolutionary History ◽  
C4 Photosynthesis ◽  
Sequence Evolution ◽  
Ancestral Branch ◽  
History Of ◽  
Grass Genomes ◽  
Protein Sequence Evolution

AbstractThe grass tribe Paniceae includes a monophyletic subclade of species, the MPC clade, which specialize in each of the three primary C4 sub-pathways NADP-ME, NAD-ME and PCK. The evolutionary history of C4 photosynthesis in this subclade remains ambiguous. Leveraging newly sequenced grass genomes and syntenic orthology data, we estimated rates of protein sequence evolution on ancestral branches for both core enzymes shared across different C4 sub-pathways and enzymes specific to C4 sub-pathways. While core enzymes show elevated rates of protein sequence evolution in ancestral branches consistent with a transition from C3 to C4 photosynthesis in the ancestor for this clade, no subtype specific enzymes showed similar patterns. At least one protein involved in photorespiration also showed elevated rates of protein sequence evolution in the ancestral branch. The set of core C4 enzymes examined here combined with the photorespiratory pathway are necessary for the C2 photosynthetic cycle, a previously proposed intermediate between C3 and C4 photosynthesis. The patterns reported here are consistent with, but not conclusive proof that, C4 photosynthesis in the MPC clade of the Paniceae evolved via a C2 intermediate.

scholarly journals Genetics of alternative splicing evolution during sunflower domestication

2018 ◽  
Vol 115 (26) ◽  
pp. 6768-6773 ◽  
Author(s):  
Chris C. R. Smith ◽  
Silas Tittes ◽  
J. Paul Mendieta ◽  
Erin Collier-zans ◽  
Heather C. Rowe ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Intron Retention ◽  
Population Divergence ◽  
Evolutionary Transition ◽  
Differential Splicing ◽  
Evolutionary Transitions ◽  
Protein Coding ◽  
Standing Variation ◽  
Splice Forms ◽  
Splicing Patterns

Alternative splicing enables organisms to produce the diversity of proteins necessary for multicellular life by using relatively few protein-coding genes. Although differences in splicing have been identified among divergent taxa, the shorter-term evolution of splicing is understudied. The origins of novel splice forms, and the contributions of alternative splicing to major evolutionary transitions, are largely unknown. This study used transcriptomes of wild and domesticated sunflowers to examine splice differentiation and regulation during domestication. We identified substantial splicing divergence between wild and domesticated sunflowers, mainly in the form of intron retention. Transcripts with divergent splicing were enriched for seed-development functions, suggesting that artificial selection impacted splicing patterns. Mapping of quantitative trait loci (QTLs) associated with 144 differential splicing cases revealed primarilytrans-acting variation affecting splicing patterns. A large proportion of identified QTLs contain known spliceosome proteins and are associated with splicing variation in multiple genes. Examining a broader set of wild and domesticated sunflower genotypes revealed that most differential splicing patterns in domesticated sunflowers likely arose from standing variation in wildHelianthus annuusand gained frequency during the domestication process. However, several domesticate-associated splicing patterns appear to be introgressed from otherHelianthusspecies. These results suggest that sunflower domestication involved selection on pleiotropic regulatory alleles. More generally, our findings indicate that substantial differences in isoform abundances arose rapidly during a recent evolutionary transition and appear to contribute to adaptation and population divergence.

ON THE THEORY OF GAMMA RAY BURSTS AND HYPERNOVAE: THE BLACK HOLE SOFT X-RAY TRANSIENT SOURCES

2003 ◽  
Vol 18 (04) ◽  
pp. 527-576 ◽  
Author(s):  
CHANG-HWAN LEE ◽  
GERALD E. BROWN
Keyword(s):  
Mass Transfer ◽  
Black Hole ◽  
Mass Loss ◽  
Evolutionary History ◽  
Main Sequence ◽  
Gamma Ray ◽  
Supernova Explosion ◽  
Sequence Evolution ◽  
X Ray ◽  
Black Hole Binaries

We show that a common evolutionary history can produce the black hole binaries in the Galaxy in which the black holes have masses of ~ 5 - 10M⊙. In the black hole binaries with low-mass, ≲ 2.5M⊙ ZAMS (zero age main sequence) companions, the latter remain in main sequence during the active stage of soft X-ray transients (SXT's), most of them being of K or M classification. In two intermediate cases, IL Lupi and Nova Scorpii with ZAMS ~ 2.5M⊙ companions the orbits are greatly widened because of large mass loss in the explosion forming the black hole, and whereas these companions are in late main sequence evolution, they are close to evolving. Binaries with companion ZAMS masses ≳ 3M⊙ are initially "silent" until the companion begins evolving across the Herzsprung gap. We provide evidence that the narrower, shorter period binaries, with companions now in main sequence, are fossil remnants of gamma ray bursters (GRB's). We also show that the GRB is generally accompanied by a hypernova explosion (a very energetic supernova explosion). We further show that the binaries with evolved companions are good models for some of the ultraluminous X-ray sources (ULX's) recently seen by Chandra in other galaxies. The great regularity in our evolutionary history, especially the fact that most of the companions of ZAMS mass ≲ 2.5M⊙ remain in main sequences as K or M stars can be explained by the mass loss in common envelope evolution to be Case C; i.e. to occur only after core He burning has finished. Since our argument for Case C mass transfer is not generally understood in the community, we add an appendix, showing that with certain assumptions which we outline we can reproduce the regularities in the evolution of black hole binaries by Case C mass transfer.

scholarly journals Deep time structural evolution of retroviral and filoviral surface envelope proteins

2021 ◽  
Author(s):  
Isidro Hotzel
Keyword(s):  
Envelope Protein ◽  
Ebola Virus ◽  
Structural Evolution ◽  
Structural Diversity ◽  
Protein Subunit ◽  
Deep Time ◽  
Host Interactions ◽  
Surface Envelope ◽  
Differential Expansion ◽  
Sandwich Core

The retroviral surface envelope protein subunit (SU) mediates receptor binding and triggers membrane fusion by the transmembrane subunit (TM). SU evolves rapidly under strong selective conditions, resulting in seemingly unrelated SU structures in highly divergent retroviruses. Structural modeling of the SU of several retroviruses and related endogenous retroviral elements with AlphaFold identifies a TM-proximal SU β-sandwich structure that has been conserved in the orthoretroviruses for at least 110 million years. The SU of orthoretroviruses diversified by differential expansion of the β-sandwich core to form domains involved in virus-host interactions. The β-sandwich domain is also conserved in the SU equivalent GP1 of Ebola virus although with a significantly different orientation in the trimeric envelope protein structure. The unified structural view of orthoretroviral SU and filoviral GP1 identifies an ancient, structurally conserved and evolvable domain underlying the structural diversity of orthoretroviral SU and filoviral GP1.

scholarly journals Advanced Cambrian hydroid fossils (Cnidaria: Hydrozoa) extend the medusozoan evolutionary history

2021 ◽  
Vol 288 (1944) ◽  
pp. 20202939
Author(s):  
Xikun Song ◽  
Bernhard Ruthensteiner ◽  
Mingxin Lyu ◽  
Xi Liu ◽  
Jian Wang ◽  
...  
Keyword(s):  
Life Histories ◽  
Morphological Traits ◽  
Evolutionary History ◽  
New Genus ◽  
Northern China ◽  
Systematic Position ◽  
Life Strategy ◽  
Late Neoproterozoic ◽  
Evolutionary Aspects ◽  
Medusa Stage

Primitive cnidarians are crucial for elucidating the early evolution of metazoan body plans and life histories in the late Neoproterozoic and Palaeozoic. The highest complexity of both evolutionary aspects within cnidarians is found in extant hydrozoans. Many colonial hydrozoans coated with chitinous exoskeletons have the potential to form fossils; however, only a few fossils possibly representing hydroids have been reported, which still require scrutiny. Here, we present an exceptionally well-preserved hydroid found in the Upper Cambrian Fengshan Formation in northern China. It was originally interpreted as a problematic graptolite with an uncertain systematic position. Based on three characteristic morphological traits shared with extant hydroids (with paired hydrothecae, regular hydrocaulus internodes and special intrathecal origin pattern of hydrocladium), we propose this fossil hydroid as a new genus, Palaeodiphasia gen. nov., affiliated with the advanced monophyletic hydrozoan clade Macrocolonia typically showing loss of the medusa stage. More Macrocolonia fossils reviewed here indicate that this life strategy of medusa loss has been achieved already as early as the Middle Devonian. The early stratigraphical appearance of such advanced hydroid contrasts with previous molecular hypotheses regarding the timing of medusozoan evolution, and may be indicative for understanding the Ediacaran cnidarian radiation.

Marine Invertebrate Larvae: Model Life Histories for Development, Ecology, and Evolution

2018 ◽  
Keyword(s):  
Conceptual Framework ◽  
Research Program ◽  
Financial Support ◽  
Life Histories ◽  
Evolutionary History ◽  
Evolutionary Ecology ◽  
Marine Invertebrate ◽  
Model Organisms ◽  
Research Questions ◽  
Invertebrate Larvae

We provide a conceptual framework for studies of the developmental and evolutionary ecology of marine invertebrate larvae and illustrate how contributions to this volume demonstrate both past achievements and the future fecundity of this research program. Our conceptual framework is anchored in the idea of model life histories, which is a category of investigation similar to but distinct from model organisms or model clades. Marine invertebrate larvae constitute a coherent, structured research program as model life histories that represent developmental, ecological, and evolutionary processes in different ways. They facilitate interdisciplinary investigation that integrates different approaches to diverse research questions about developmental mechanisms, evolutionary history, and adaptation, as well as providing a window on alterations of the marine environment due to anthropogenic climate change. Success in studies of model life histories provides a strong case for sustained professional, institutional, and financial support to carry these endeavors forward.

Alternative Splicing and Disease

2009 ◽  
pp. 291-310
Author(s):  
Heike Stier
Keyword(s):  
Gene Expression ◽  
Cystic Fibrosis ◽  
Alternative Splicing ◽  
Muscular Atrophy ◽  
Splicing Factor ◽  
Beta Thalassemia ◽  
Splicing Factors ◽  
Correct Function ◽  
Minor Sequence ◽  
Splice Forms

Alternative splicing is an important part of the regular process of gene expression. It controls time and tissue dependent expression of specific splice forms and depends on the correct function of about 100 splicing factor proteins of which many are the product of alternative splicing itself. It is therefore not surprising that even minor sequence disturbances can cause mis-spliced gene products with pathological effects. We survey some common diseases which can be traced back to a malfunction of alternative splicing including cystic fibrosis, beta-thalassemia, spinal muscular atrophy and cancer. Often cancer also results from even mis-spliced splicing factors leading to randomly spliced non-functional isoforms of several genes.

scholarly journals Amphibian Hormones, Calcium Physiology, Bone Weight, and Lung Use Call for a More Inclusive Approach to Understanding Ossification Sequence Evolution

2021 ◽  
Vol 9 ◽  
Author(s):  
Christopher S. Rose
Keyword(s):  
Life Histories ◽  
Skeletal Development ◽  
Sequence Evolution ◽  
Larval Habitats ◽  
Inclusive Approach ◽  
Embryonic Origin ◽  
Ossification Sequences ◽  
Ossification Process ◽  
And Behavior ◽  
Ossification Sequence

Skeleton plays a huge role in understanding how vertebrate animals have diversified in phylogeny, ecology and behavior. Recent evo-devo research has used ossification sequences to compare skeletal development among major groups, to identify conserved and labile aspects of a sequence within a group, to derive ancestral and modal sequences, and to look for modularity based on embryonic origin and type of bone. However, questions remain about how to detect and order bone appearances, the adaptive significance of ossification sequences and their relationship to adult function, and the utility of categorizing bones by embryonic origin and type. Also, the singular focus on bone appearances and the omission of other tissues and behavioral, ecological and life history events limit the relevance of such analyses. Amphibians accentuate these concerns because of their highly specialized biphasic life histories and the exceptionally late timing, and high variability of their ossification sequences. Amphibians demonstrate a need for a whole-animal, whole-ontogeny approach that integrates the entire ossification process with physiology, behavior and ecology. I discuss evidence and hypotheses for how hormone mediation and calcium physiology might elicit non-adaptive variability in ossification sequence, and for adaptive strategies to partition larval habitats using bone to offset the buoyancy created by lung use. I also argue that understanding plasticity in ossification requires shifting focus away from embryonic development and adult function, and toward postembryonic mechanisms of regulating skeletal growth, especially ones that respond directly to midlife environments and behaviors.

Genome-Wide Analysis of Alternative Splicing Points to Novel Leukemia Relevant Genes in Acute Myeloid Leukemia.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 2391-2391
Author(s):  
Anna Dolnik ◽  
Andreas Gerhardinger ◽  
Ursula Botzenhardt ◽  
Sabrina Heinrich ◽  
Richard Schlenk ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Myeloid Leukemia ◽  
Splice Variants ◽  
Cell Cycle Control ◽  
Rt Pcr ◽  
Genome Wide ◽  
Alternatively Spliced ◽  
Splice Forms ◽  
Exon Microarray ◽  
Acute Myeloid

Abstract Abstract 2391 Poster Board II-368 Alternative mRNA splicing represents an effective mechanism of regulating gene function as well as a key element to increase the coding capacity of the human genome. Today, an increasing number of reports illustrates that aberrant splicing events can contribute to human disease and that alterations in the splicing machinery are common and functionally important for cancer development. Aberrant splice forms can for example have genome-wide effects by deregulating key signaling pathways. However, for most of the aberrant mRNA transcripts detected it remains unclear whether they directly contribute to the malignant phenotype or just represent a by-product of cellular transformation. Thus, more comprehensive analyses of the transcriptome splicing are warranted in order to get novel insights into the biology underlying malignancies like, e.g., acute myeloid leukemia (AML). Here, we performed a genome-wide screening of splicing events in AML using the Exon microarray platform GeneChip Human Exon 1.0 ST (Affymetrix). We analyzed forty AML cases with complex karyotypes and twenty Core Binding Factor (CBF) AML cases (entered on a multicenter trial for patients <60 years, AMLSG 07-04) using this microarray approach allowing the detection of splice variants. In order to detect alternative splicing events distinguishing different leukemia subgroups we applied a commercial and an open source software tool: XRAY version 3.9 (Biotique Systems) and the OneChannelGUI package for R (version 1.10.7 available at http://www.bioinformatica.unito.it/oneChannelGUI/). Using XRAY supervised analysis comparing subgroups of CBF and complex karyotype AML we identified 1120 transcripts to be potentially alternatively spliced. In parallel, the analysis of the same AML subgroups using the OneChannelGUI package in R revealed 1439 candidates with an overlap of only 211 genes. Of these transcripts, that have been indicated by both programs as potentially alternatively spliced, selected candidates were further investigated by RT-PCR, quantitative RT-PCR and sequence analysis for the presence of splice-variants. Of 26 candidate genes studied, we could confirm alternative splice forms for 5 genes that might potentially be involved in driving leukemogenesis, such as the protein coding gene arginine methyltransferase 1 (PRMT1), which regulates transcription through histone methylation and participates in DNA damage response. Furthermore, we could confirm differential exon usage in the protein tyrosine phosphatase non-receptor type (PTPN6) transcript, which encodes for a negative regulator of numerous signaling pathways involved in cell cycle control and apoptosis. Similarly, the mRNA of the protein Rho GTPase activating protein 4 (ARHGAP4), which has been shown to regulate cell motility, was alternatively spliced between CBF and complex karyotype subgroups. In summary, these first gene expression data demonstrate that the attempt to elucidate the splicing of transcriptome in AML by applying Exon microarray technology is challenging in particular with regard to the currently available software solutions. Nevertheless, our results show that this approach offers the ability to detect novel alternatively spliced candidate genes. Being involved in cell cycle control, regulation of transcription or remodeling of the cytoskeleton, alternative splicing of these genes might play a potential role in the pathomechanism of distinct AML subgroups. Thus, in the future more extensive Exon array profiling with more sophisticated software solutions at hand is likely to provide additional insights into the molecular mechanisms of leukemogenesis and might reveal novel targets for refined therapeutic strategies in AML. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Transcripts' evolutionary history and structural dynamics give mechanistic insights into the functional diversity of the JNK family.

2017 ◽  
Author(s):  
Adel Ait-hamlat ◽  
Diego Javier Zea ◽  
Antoine Labeeuw ◽  
Lelia Polit ◽  
Hugues Richard ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Structural Dynamics ◽  
Evolutionary History ◽  
Protein Isoforms ◽  
Computational Tool ◽  
Tertiary Structures ◽  
Transcript Isoforms ◽  
History Of ◽  
Transcription Sites ◽  
Splicing Isoforms

Alternative splicing and alternative initiation/termination transcription sites, have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to protein evolution and their impact at the protein structure level. Here, we address both issues by reconstructing the evolutionary history of transcripts and by modeling the tertiary structures of the corresponding protein isoforms. We reconstruct phylogenetic forests relating 60 transcripts from the c-Jun N-terminal kinase (JNK) family observed in 7 species. We identify two alternative splicing events of ancient origin and show that they induce subtle changes on the protein's structural dynamics. We highlight a previously uncharacterized transcript whose predicted structure seems stable in solution. We further demonstrate that orphan transcripts, for which no phylogeny could be reconstructed, display peculiar sequence and structural properties. Our approach is implemented in PhyloSofS (Phylogenies of Splicing Isoforms Structures), a fully automated computational tool freely available at https://github.com/PhyloSofS-Team/PhyloSofS.

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