scholarly journals Novel Molecular Signatures in the PIP4K/PIP5K Family of Proteins Specific for Different Isozymes and Subfamilies Provide Important Insights into the Evolutionary Divergence of this Protein Family

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 312 ◽  
Author(s):  
Bijendra Khadka ◽  
Radhey S. Gupta
Keyword(s):  
Molecular Markers ◽  
Species Distribution ◽  
Common Ancestor ◽  
Protein Sequences ◽  
Distribution Patterns ◽  
Duplication Event ◽  
Evolutionary Divergence ◽  
Secondary Messenger ◽  
Conserved Signature Indels ◽  
Eukaryotic Organisms

Members of the PIP4K/PIP5K family of proteins, which generate the highly important secondary messenger phosphatidylinositol-4,5-bisphosphate, play central roles in regulating diverse signaling pathways. In eukaryotic organisms, multiple isozymes and subfamilies of PIP4K/PIP5K proteins are found and it is of much interest to understand their evolution and species distribution and what unique molecular and biochemical characteristics distinguish specific isozymes and subfamilies of proteins. We report here the species distribution of different PIP4K/PIP5K family of proteins in eukaryotic organisms and phylogenetic analysis based on their protein sequences. Our results indicate that the distinct homologs of both PIP4K and PIP5K are found in different organisms belonging to the Holozoa clade of eukaryotes, which comprises of various metazoan phyla as well as their close unicellular relatives Choanoflagellates and Filasterea. In contrast, the deeper-branching eukaryotic lineages, as well as plants and fungi, contain only a single homolog of the PIP4K/PIP5K proteins. In parallel, our comparative analyses of PIP4K/PIP5K protein sequences have identified six highly-specific molecular markers consisting of conserved signature indels (CSIs) that are uniquely shared by either the PIP4K or PIP5K proteins, or both, or specific subfamilies of these proteins. Of these molecular markers, 2 CSIs are distinctive characteristics of all PIP4K homologs, 1 CSI distinguishes the PIP4K and PIP5K homologs from the Holozoa clade of species from the ancestral form of PIP4K/PIP5K found in deeper-branching eukaryotic lineages. The remaining three CSIs are specific for the PIP5Kα, PIP5Kβ, and PIP4Kγ subfamilies of proteins from vertebrate species. These molecular markers provide important means for distinguishing different PIP4K/PIP5K isozymes as well as some of their subfamilies. In addition, the distribution patterns of these markers in different isozymes provide important insights into the evolutionary divergence of PIP4K/PIP5K proteins. Our results support the view that the Holozoa clade of eukaryotic organisms shared a common ancestor exclusive of the other eukaryotic lineages and that the initial gene duplication event leading to the divergence of distinct types of PIP4K and PIP5K homologs occurred in a common ancestor of this clade. Based on the results gleaned from different studies presented here, a model for the evolutionary divergence of the PIP4K/PIP5K family of proteins is presented.

Vegetation dynamics and species distribution patterns in the inland desert wadis of South Sinai, Egypt

2013 ◽  
Vol 39 (2) ◽  
pp. 93-110
Author(s):  
Fawzy M. Salama ◽  
Monier Abd El-Ghani ◽  
Salah El Naggar ◽  
Mohamed Aljarroushi
Keyword(s):  
Species Distribution ◽  
Vegetation Dynamics ◽  
Distribution Patterns ◽  
South Sinai

Levels of Spatial Variability: The “Community” Problem

1990 ◽  
Vol 5 ◽  
pp. 13-30 ◽  
Author(s):  
D. A. Springer ◽  
A. I. Miller
Keyword(s):  
Community Structure ◽  
Spatial Variability ◽  
Species Distribution ◽  
Distribution Patterns ◽  
The Past ◽  
Structure And Dynamics ◽  
Evolutionary Units ◽  
The Way

The way we view species distribution patterns, particularly at the level commonly referred to as the “community”, has changed over the past 70 years in biology and, subsequently, in paleontology. Because the degree to which species associations can be interpreted as ecological and evolutionary units depends ultimately on recognition and interpretation of faunal spatial variability, we need to understand the nature of this variability at all levels of resolution before we can adequately address questions of “community” structure and dynamics. While it is possible to recognize spatial variability at several levels, from the distributions of individuals within a species to the overall pattern created by the global biota, we must ask whether these patterns really comprise a hierarchy with natural discontinuities (Fig. 1), or whether it is more realistic to view them as a continuous variability spectrum.

scholarly journals Squalene-Hopene Cyclases

2011 ◽  
Vol 77 (12) ◽  
pp. 3905-3915 ◽  
Author(s):  
Gabriele Siedenburg ◽  
Dieter Jendrossek
Keyword(s):  
Common Ancestor ◽  
Amino Acid Sequences ◽  
Enzymatic Reactions ◽  
Covalent Bonds ◽  
Content Type ◽  
Oxidosqualene Cyclase ◽  
Ring Structures ◽  
One Step ◽  
Alicyclobacillus Acidocaldarius ◽  
Eukaryotic Organisms

ABSTRACTHopanoids and sterols are members of a large group of cyclic triterpenoic compounds that have important functions in many prokaryotic and eukaryotic organisms. They are biochemically synthesized from linear precursors (squalene, 2,3-oxidosqualene) in only one enzymatic step that is catalyzed by squalene-hopene cyclase (SHC) or oxidosqualene cyclase (OSC). SHCs and OSCs are related in amino acid sequences and probably are derived from a common ancestor. The SHC reaction requires the formation of five ring structures, 13 covalent bonds, and nine stereo centers and therefore is one of the most complex one-step enzymatic reactions. We summarize the knowledge of the properties of triterpene cyclases and details of the reaction mechanism ofAlicyclobacillus acidocaldariusSHC. Properties of other SHCs are included.

scholarly journals The closely related Drosophila sry beta and sry delta zinc finger proteins show differential embryonic expression and distinct patterns of binding sites on polytene chromosomes

Development ◽  
1990 ◽  
Vol 110 (1) ◽  
pp. 141-149 ◽  
Author(s):  
F. Payre ◽  
S. Noselli ◽  
V. Lefrere ◽  
A. Vincent
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Polytene Chromosomes ◽  
Duplication Event ◽  
Amino Acid Sequences ◽  
Evolutionary Divergence ◽  
Coding Region ◽  
Protein Coding

Serendipity (sry) beta (beta) and delta (delta) are two finger protein genes resulting from a duplication event. Comparison of their respective protein products shows interspersed blocks of conserved and divergent amino-acid sequences. The most extensively conserved region corresponds to the predicted DNA-binding domain which includes 6 contiguous fingers; no significant sequence conservation is found upstream and downstream of the protein-coding region. We have analysed the evolutionary divergence of the sry beta and delta proteins on two separate levels, their embryonic pattern of expression and their DNA-binding properties in vitro and in vivo. By using specific antibodies and transformant lines containing beta-galactosidase fusion genes, we show that the sry beta and sry delta proteins are maternally inherited and present in embryonic nuclei at the onset of zygotic transcription, suggesting that they are transcription factors involved in this process. Zygotic synthesis of the sry beta protein starts during nuclear division cycles 12–13, prior to cellularisation of the blastoderm, while the zygotic sry delta protein is not detectable before germ band extension (stage 10 embryos). Contrary to sry delta, the zygotic sry beta protein constitutes only a minor fraction of the total embryonic protein. The sry beta and delta proteins made in E. coli bind to DNA, with partly overlapping specificities. Their in vivo patterns of binding to DNA, visualised by immunostaining polytene chromosomes, differ both in the number and position of their binding sites. Thus changes in expression pattern and DNA-binding specificity have contributed to the evolution of the sry beta and delta genes.

The saltmarsh vegetation of the lower Berg River

Bothalia ◽  
1994 ◽  
Vol 24 (2) ◽  
pp. 223-228
Author(s):  
M. O'Callaghan
Keyword(s):  
Sea Level ◽  
Species Distribution ◽  
Distribution Patterns ◽  
Competitive Interactions ◽  
Tidal Inundation ◽  
Mean Sea Level ◽  
Irregular Distribution ◽  
Vegetation Species

The lower Berg River supports approximately 250 ha of estuarine saltmarsh vegetation. Species distribution patterns, as sampled along six transects, are described. Elevation above mean sea level (MSL) is proposed as a strong determinant of these patterns. However, there are no typical patterns. The patchy and irregular distribution patterns possibly result from an inconsistent relationship between species distribution and salinity, tidal inundation and/or competitive interactions.

scholarly journals Novel Molecular Synapomorphies Demarcate Different Main Groups/Subgroups of Plasmodium and Piroplasmida Species Clarifying Their Evolutionary Relationships

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 490 ◽  
Author(s):  
Sharma ◽  
Gupta
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Plasmodium Species ◽  
Protein Sequences ◽  
Evolutionary Relationships ◽  
Major Life ◽  
Comparative Analyses ◽  
Large Numbers ◽  
Conserved Signature Indels ◽  
Relationship Of

The class Hematozoa encompasses several clinically important genera, including Plasmodium, whose members cause the major life-threating disease malaria. Hence, a good understanding of the interrelationships of organisms from this class and reliable means for distinguishing them are of much importance. This study reports comprehensive phylogenetic and comparative analyses on protein sequences on the genomes of 28 hematozoa species to understand their interrelationships. In addition to phylogenetic trees based on two large datasets of protein sequences, detailed comparative analyses were carried out on the genomes of hematozoa species to identify novel molecular synapomorphies consisting of conserved signature indels (CSIs) in protein sequences. These studies have identified 79 CSIs that are exclusively present in specific groups of Hematozoa/Plasmodium species, also supported by phylogenetic analysis, providing reliable means for the identification of these species groups and understanding their interrelationships. Of these CSIs, six CSIs are specifically shared by all hematozoa species, two CSIs serve to distinguish members of the order Piroplasmida, five CSIs are uniquely found in all Piroplasmida species except B. microti and two CSIs are specific for the genus Theileria. Additionally, we also describe 23 CSIs that are exclusively present in all genome-sequenced Plasmodium species and two, nine, ten and eight CSIs which are specific for members of the Plasmodium subgenera Haemamoeba, Laverania, Vinckeia and Plasmodium (excluding P. ovale and P. malariae), respectively. Additionally, our work has identified several CSIs that support species relationships which are not evident from phylogenetic analysis. Of these CSIs, one CSI supports the ancestral nature of the avian-Plasmodium species in comparison to the mammalian-infecting groups of Plasmodium species, four CSIs strongly support a specific relationship of species between the subgenera Plasmodium and Vinckeia and three CSIs each that reliably group P. malariae with members of the subgenus Plasmodium and P. ovale within the subgenus Vinckeia, respectively. These results provide a reliable framework for understanding the evolutionary relationships among the Plasmodium/Piroplasmida species. Further, in view of the exclusivity of the described molecular markers for the indicated groups of hematozoa species, particularly large numbers of unique characteristics that are specific for all Plasmodium species, they provide important molecular tools for biochemical/genetic studies and for developing novel diagnostics and therapeutics for these organisms.

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