scholarly journals Structural Changes and Adaptative Evolutionary Constraints In FLOWERING LOCUS T and TERMINAL FLOWER1-Like Genes of Flowering Plants

2021 ◽  
Author(s):  
Deivid Almeida de Jesus ◽  
Darlisson Mesquista Batista ◽  
Shayla Salzman ◽  
Lucas Miguel Carvalho ◽  
Kaue Santana ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Structural Changes ◽  
Protein Structures ◽  
Flowering Phenology ◽  
Flowering Locus T ◽  
Ancestral Sequences ◽  
Terminal Flower 1 ◽  
History Of ◽  
Flowering Locus ◽  
Complex Signaling

Abstract Regulation of flowering is a crucial event in the evolutionary history of angiosperms. The production of flowers is regulated through the integration of different environmental and endogenous stimuli, many of which involve the activation of different genes in a hierarchical and complex signaling network. The FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1) gene family is known to regulate important aspects of flowering in plants. To better understand the pivotal events that changed FT and TFL1 functions during the evolution of angiosperms, we reconstructed the ancestral sequences of FT/TFL1-like genes and predicted protein structures to identify determinant sites that evolved in both proteins and allowed the adaptative diversification in the flowering phenology and developmental processes. Residues from the P-loop domain of the analyzed FT structures showed predominantly high destabilizing mutations which is consistent with constant selective pressure found for this region. In addition, we demonstrate that the occurrence of destabilizing mutations in residues located at the phosphatidylcholine binding sites of FT structure experience positive selection, and some residues of 4th exon are under negative selection, which is compensated by the occurrence of stabilizing mutations in key regions and the P-loop to maintain the overall protein stability. Our results shed light on the evolutionary history of key genes involved in the diversification of angiosperms.

scholarly journals Computational design of symmetrical eight-bladed β-propeller proteins

IUCrJ ◽  
2019 ◽  
Vol 6 (1) ◽  
pp. 46-55 ◽  
Author(s):  
Hiroki Noguchi ◽  
Christine Addy ◽  
David Simoncini ◽  
Staf Wouters ◽  
Bram Mylemans ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Evolutionary History ◽  
Protein Complexes ◽  
Protein A ◽  
Protein Structures ◽  
Computational Design ◽  
Computational Approach ◽  
Modular Architecture ◽  
Cellular Processes ◽  
History Of

β-Propeller proteins form one of the largest families of protein structures, with a pseudo-symmetrical fold made up of subdomains called blades. They are not only abundant but are also involved in a wide variety of cellular processes, often by acting as a platform for the assembly of protein complexes. WD40 proteins are a subfamily of propeller proteins with no intrinsic enzymatic activity, but their stable, modular architecture and versatile surface have allowed evolution to adapt them to many vital roles. By computationally reverse-engineering the duplication, fusion and diversification events in the evolutionary history of a WD40 protein, a perfectly symmetrical homologue called Tako8 was made. If two or four blades of Tako8 are expressed as single polypeptides, they do not self-assemble to complete the eight-bladed architecture, which may be owing to the closely spaced negative charges inside the ring. A different computational approach was employed to redesign Tako8 to create Ika8, a fourfold-symmetrical protein in which neighbouring blades carry compensating charges. Ika2 and Ika4, carrying two or four blades per subunit, respectively, were found to assemble spontaneously into a complete eight-bladed ring in solution. These artificial eight-bladed rings may find applications in bionanotechnology and as models to study the folding and evolution of WD40 proteins.

scholarly journals The FLOWERING LOCUS T/TERMINAL FLOWER 1 Family in Lombardy Poplar

2008 ◽  
Vol 49 (3) ◽  
pp. 291-300 ◽  
Author(s):  
Tomohiro Igasaki ◽  
Yumiko Watanabe ◽  
Mitsuru Nishiguchi ◽  
Nobuhiro Kotoda
Keyword(s):  
Flowering Locus T ◽  
Terminal Flower ◽  
Terminal Flower 1 ◽  
Flowering Locus ◽  
Lombardy Poplar

Identification and Characterization of the FLOWERING LOCUS T/TERMINAL FLOWER 1 Gene Family in Petunia

2019 ◽  
Vol 38 (9) ◽  
pp. 982-995 ◽  
Author(s):  
Lan Wu ◽  
Fei Li ◽  
Qiaohong Deng ◽  
Sisi Zhang ◽  
Qin Zhou ◽  
...  
Keyword(s):  
Gene Family ◽  
Flowering Locus T ◽  
Terminal Flower ◽  
Terminal Flower 1 ◽  
Flowering Locus ◽  
Identification And Characterization

scholarly journals Reconstructing the Evolutionary History of Nitrogenases: Evidence for Ancestral Molybdenum-Cofactor Utilization

2019 ◽  
Author(s):  
Amanda K. Garcia ◽  
Hanon McShea ◽  
Bryan Kolaczkowski ◽  
Betül Kaçar
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Reconstruction ◽  
Fixed Nitrogen ◽  
Ancestral Sequences ◽  
Cofactor Biosynthesis ◽  
Ancient Proteins ◽  
History Of ◽  
Femo Cofactor ◽  
Global Biogeochemical Cycles ◽  
Active Site Sequence

ABSTRACTThe nitrogenase metalloenzyme family, essential for supplying fixed nitrogen to the biosphere, is one of life’s key biogeochemical innovations. The three isozymes of nitrogenase differ in their metal dependence, each binding either a FeMo-, FeV-, or FeFe-cofactor where the reduction of dinitrogen takes place. The history of nitrogenase metal dependence has been of particular interest due to the possible implication that ancient marine metal availabilities have significantly constrained nitrogenase evolution over geologic time. Here, we reconstructed the evolutionary history of nitrogenases, and combined phylogenetic reconstruction, ancestral sequence inference, and structural homology modeling to evaluate the potential metal dependence of ancient nitrogenases. We find that active-site sequence features can reliably distinguish extant Mo-nitrogenases from V- and Fe-nitrogenases, and that inferred ancestral sequences at the deepest nodes of the phylogeny suggest these ancient proteins most resemble modern Mo-nitrogenases. Taxa representing early-branching nitrogenase lineages lack one or more biosynthetic nifE and nifN genes that both contribute to the assembly of the FeMo-cofactor in studied organisms, suggesting that early Mo-nitrogenases may have utilized an alternate and/or simplified pathway for cofactor biosynthesis. Our results underscore the profound impacts that protein-level innovations likely had on shaping global biogeochemical cycles throughout the Precambrian, in contrast to organism-level innovations that characterize the Phanerozoic Eon.

Karyotype evolution in the Pinaceae: implication with molecular phylogeny

Genome ◽  
2012 ◽  
Vol 55 (11) ◽  
pp. 735-753 ◽  
Author(s):  
K.K. Nkongolo ◽  
M. Mehes-Smith
Keyword(s):  
Evolutionary History ◽  
Structural Changes ◽  
Karyotype Evolution ◽  
Diploid Species ◽  
Telomeric Sequence ◽  
The Family ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Numeric Data

The family Pinaceae is made up mostly of diploid species (2n = 24). Systematization of karyotype analysis was developed to make comparison of intra- and interspecific karyotypes among the Pinaceae more accurate and reliable. Considering all parameters, the genera Pseudotsuga and Pseudolarix have the “most derived” (or advanced) and asymmetric karyotypes in the Pinaceae, followed by Larix, Picea, Abies, and Cedrus. The genus Pinus was the “least derived” (or ancestral) of all the genera of the Pinaceae analyzed. Differences in karyotype formulae and asymmetry indices were found among species within the same genera, suggesting that structural changes may have contributed to the diversification of the genus. This review is a detailed analysis of comparative karyotyping based on similar parameters, including numeric data and cytogenetic information. Telomeric sequence repeats and rDNA distribution in the Pinaceae were surveyed. The role of transposition in rDNA chromosome distribution is analyzed. Cytogenetic implications of hybridization between related species are reported. Likewise, the relationships between molecular phylogenetic and karyotype evolution is discussed in light of several reports. Within many genera, chromosomal organization was conserved despite independent molecular divergence and adaptation through the evolutionary history of the species of the Pinaceae.

scholarly journals Episodes of Rapid Recovery of the Functional Activity of the ras85D Gene in the Evolutionary History of Phylogenetically Distant Drosophila Species

2022 ◽  
Vol 12 ◽  
Author(s):  
A. I. Chekunova ◽  
S. Yu. Sorokina ◽  
E. A. Sivoplyas ◽  
G. N. Bakhtoyarov ◽  
P. A. Proshakov ◽  
...  
Keyword(s):  
Functional Activity ◽  
Promoter Region ◽  
Evolutionary History ◽  
Structural Changes ◽  
Regulatory Region ◽  
Evolutionary Origin ◽  
Regulatory Sequences ◽  
Structural Rearrangements ◽  
Evolutionary Variation ◽  
History Of

As assemblies of genomes of new species with varying degrees of relationship appear, it becomes obvious that structural rearrangements of the genome, such as inversions, translocations, and transposon movements, are an essential and often the main source of evolutionary variation. In this regard, the following questions arise. How conserved are the regulatory regions of genes? Do they have a common evolutionary origin? And how and at what rate is the functional activity of genes restored during structural changes in the promoter region? In this article, we analyze the evolutionary history of the formation of the regulatory region of the ras85D gene in different lineages of the genus Drosophila, as well as the participation of mobile elements in structural rearrangements and in the replacement of specific areas of the promoter region with those of independent evolutionary origin. In the process, we substantiate hypotheses about the selection of promoter elements from a number of frequently repeated motifs with different degrees of degeneracy in the ancestral sequence, as well as about the restoration of the minimum required set of regulatory sequences using a conversion mechanism or similar.

Evidence for local DNA influences on patterns of substitutions in the human α-interferon gene family

1986 ◽  
Vol 28 (4) ◽  
pp. 483-496 ◽  
Author(s):  
G. Brian Golding ◽  
Barry W. Glickman
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
Spontaneous Mutation ◽  
Direct Repeat ◽  
Base Substitution ◽  
Human Interferon ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Ancestral Sequences ◽  
History Of

The evolutionary history of genes can be used to examine patterns of spontaneous mutation if the sequences are sufficiently extensive to provide reliable data. Many human α-interferon genes have been sequenced and they form a large multigene family including several pseudogenes. A phylogenetic history for 15 human interferon sequences was reconstructed and their ancestral sequences inferred using a maximum parsimony method. This evolutionary history provided a record of more than 738 spontaneous mutations that have occurred in man's recent evolution. Of these mutations, more than 267 base substitution and deletion–insertion events were analyzed to determine the possible effects of nearby DNA sequences. Many substitutions occur at the end of long runs of identical bases and some dinucleotide pairs may mutate more often than others. Because templating by local DNA sequences has been implicated in prokaryotic mutation, the sequences were also examined for nearby repeats that include the substituted nucleotide and hence are potentially capable of templating the substitution. The majority of sequence alterations examined have either a similar direct repeat or palindrome nearby. Often such templates can account for simultaneous multiple mutations. These results suggest that sequence-directed events may occur occasionally in eukaryotes and that neighbouring DNA sequences can influence both the occurrence and types of mutations in several different ways.Key words: spontaneous mutation, template-directed mutations, phylogenetic history, evolution.

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