The plastid NAD(P)H dehydrogenase-like complex: structure, function and evolutionary dynamics

2019 ◽  
Vol 476 (19) ◽  
pp. 2743-2756 ◽  
Author(s):  
Deserah D. Strand ◽  
Lucio D'Andrea ◽  
Ralph Bock
Keyword(s):  
Evolutionary Dynamics ◽  
Selective Pressure ◽  
Complex Structure ◽  
Protonmotive Force ◽  
Large Protein ◽  
Large Protein Complex ◽  
Atp Generation ◽  
Ndh Genes ◽  
Phylogenetic Lineages ◽  
Rule Out

Abstract The thylakoid NAD(P)H dehydrogenase-like (NDH) complex is a large protein complex that reduces plastoquinone and pumps protons into the lumen generating protonmotive force. In plants, the complex consists of both nuclear and chloroplast-encoded subunits. Despite its perceived importance for stress tolerance and ATP generation, chloroplast-encoded NDH subunits have been lost numerous times during evolution in species occupying seemingly unrelated environmental niches. We have generated a phylogenetic tree that reveals independent losses in multiple phylogenetic lineages, and we use this tree as a reference to discuss possible evolutionary contexts that may have relaxed selective pressure for retention of ndh genes. While we are still yet unable to pinpoint a singular specific lifestyle that negates the need for NDH, we are able to rule out several long-standing explanations. In light of this, we discuss the biochemical changes that would be required for the chloroplast to dispense with NDH functionality with regards to known and proposed NDH-related reactions.

scholarly journals Reverse transcriptase sequences from mulberry LTR retrotransposons: characterization analysis

2017 ◽  
Vol 12 (1) ◽  
pp. 266-276
Author(s):  
Bi Ma ◽  
Lulu Kuang ◽  
Youchao Xin ◽  
Fei Hou ◽  
Ningjia He
Keyword(s):  
Reverse Transcriptase ◽  
Evolutionary Dynamics ◽  
Selective Pressure ◽  
Sequence Divergence ◽  
Degenerate Primers ◽  
Random Mutation ◽  
Functional Studies ◽  
Study Support ◽  
Element Transfer

AbstractCopia and Gypsy play important roles in structural, functional and evolutionary dynamics of plant genomes. In this study, a total of 106 and 101, Copia and Gypsy reverse transcriptase (rt) were amplified respectively in the Morus notabilis genome using degenerate primers. All sequences exhibited high levels of heterogeneity, were rich in AT and possessed higher sequence divergence of Copia rt in comparison to Gypsy rt. Two reasons are likely to account for this phenomenon: a) these elements often experience deletions or fragmentation by illegitimate or unequal homologous recombination in the transposition process; b) strong purifying selective pressure drives the evolution of these elements through “selective silencing” with random mutation and eventual deletion from the host genome. Interestingly, mulberry rt clustered with other rt from distantly related taxa according to the phylogenetic analysis. This phenomenon did not result from horizontal transposable element transfer. Results obtained from fluorescence in situ hybridization revealed that most of the hybridization signals were preferentially concentrated in pericentromeric and distal regions of chromosomes, and these elements may play important roles in the regions in which they are found. Results of this study support the continued pursuit of further functional studies of Copia and Gypsy in the mulberry genome.

scholarly journals Genomic evidence of adaptive evolution in the reptilian SOCS gene family

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11677
Author(s):  
Tian Xia ◽  
Lei Zhang ◽  
Guolei Sun ◽  
Xiufeng Yang ◽  
Honghai Zhang
Keyword(s):  
Negative Selection ◽  
Molecular Mechanisms ◽  
Evolutionary Dynamics ◽  
Theoretical Foundation ◽  
Selective Pressure ◽  
Rapid Evolution ◽  
Cytokine Signaling ◽  
Signal Pathways ◽  
Branch Model ◽  
Comprehensive Study

The suppressor of the cytokine signaling (SOCS) family of proteins play an essential role in inhibiting cytokine receptor signaling by regulating immune signal pathways. Although SOCS gene functions have been examined extensively, no comprehensive study has been performed on this gene family’s molecular evolution in reptiles. In this study, we identified eight canonical SOCS genes using recently-published reptilian genomes. We used phylogenetic analysis to determine that the SOCS genes had highly conserved evolutionary dynamics that we classified into two types. We identified positive SOCS4 selection signals in whole reptile lineages and SOCS2 selection signals in the crocodilian lineage. Selective pressure analyses using the branch model and Z-test revealed that these genes were under different negative selection pressures compared to reptile lineages. We also concluded that the nature of selection pressure varies across different reptile lineages on SOCS3, and the crocodilian lineage has experienced rapid evolution. Our results may provide a theoretical foundation for further analyses of reptilian SOCS genes’ functional and molecular mechanisms, as well as their roles in reptile growth and development.

scholarly journals Identification of multiple TAR DNA Binding Protein retropseudogene lineages during the evolution of primates

2021 ◽  
Author(s):  
Juan Opazo ◽  
Kattina Zavala ◽  
Luis Vargas-Chacoff ◽  
Francisco Morera ◽  
Gonzalo Mardones
Keyword(s):  
Dna Binding ◽  
Evolutionary History ◽  
Evolutionary Dynamics ◽  
Binding Protein ◽  
Genetic Material ◽  
Dna Binding Protein ◽  
Functional Protein ◽  
Species Specific ◽  
Regulatory Functions ◽  
Rule Out

The TAR DNA Binding Protein (TARDBP) gene has gained attention in biomedicine after the discovery of several pathogenic mutations. The lack of knowledge about its evolutionary history contrasts with a large number of studies in the biomedical area. This study aimed to investigate the retrotransposition evolutionary dynamics associated with this gene in primates. We identified retropseudogenes that originated in the ancestors of anthropoids, catarrhines, and lemuriformes, i.e. the strepsirrhine clade that inhabit Madagascar. We also found species-specific retropseudogenes in the philippine tarsier, Bolivian squirrel monkey, capuchin monkey and vervet. Although retropseudogenes are not able to produce a functional protein, we can not rule out that they may represent genetic material upon which evolution acts on, especially with regulatory functions.

scholarly journals Genetic Diversity of the Streptococcal Competence (com) Gene Locus

1999 ◽  
Vol 181 (10) ◽  
pp. 3144-3154 ◽  
Author(s):  
Adrian M. Whatmore ◽  
Victoria A. Barcus ◽  
Christopher G. Dowson
Keyword(s):  
Gene Locus ◽  
Bacterial Population ◽  
Selective Pressure ◽  
Response Regulator ◽  
Clear Correlation ◽  
Potential Source ◽  
Sequence Variations ◽  
Two Component ◽  
Streptococcal Species ◽  
Rule Out

ABSTRACT The com operon of naturally transformable streptococcal species contains three genes, comC, comD, andcomE, involved in the regulation of competence. ThecomC gene encodes a competence-stimulating peptide (CSP) thought to induce competence in the bacterial population at a critical extracellular concentration. The comD and comEgenes are believed to encode the transmembrane histidine kinase and response regulator proteins, respectively, of a two-component regulator, with the comD-encoded protein being a receptor for CSP. Here we report on the genetic variability of comCand comD within Streptococcus pneumoniaeisolates. Comparative analysis of sequence variations ofcomC and comD shows that, despite evidence for horizontal gene transfer at this locus and the lack of transformability of many S. pneumoniae strains in the laboratory, there is a clear correlation between the presence of a particular comCallele and the cognate comD allele. These findings effectively rule out the possibility that the presence of noncognatecomC and comD alleles may be responsible for the inability to induce competence in many isolates and indicate the importance of a functional com pathway in these isolates. In addition, we describe a number of novel CSPs from disease-associated strains of S. mitis and S. oralis. The CSPs from these isolates are much more closely related to those fromS. pneumoniae than to most CSPs previously reported fromS. mitis and S. oralis, suggesting that these particular organisms may be a potential source of DNA in recombination events generating the mosaic structures commonly reported in genes ofS. pneumoniae that are under strong selective pressure.

scholarly journals A pairing of parental noroviruses with unequal competitiveness provides a clear advantage for emergence of progeny recombinants

2020 ◽  
Author(s):  
Eung Seo Koo ◽  
Yong Seok Jeong
Keyword(s):  
Mixed Infection ◽  
Human Population ◽  
Selective Pressure ◽  
Genetic Recombination ◽  
Sampling Period ◽  
Theoretical Concept ◽  
Human Norovirus ◽  
Detection Frequency ◽  
Phylogenetic Lineages ◽  
Relative Detection

Genetic recombination plays a pivotal role in the appearance of human norovirus recombinants that cause global epidemics. However, the factors responsible for the appearance of these recombinants remains largely unknown. In this study, we revealed a selective pressure that restricts parental combinations leading to the emergence of norovirus recombinants. To investigate traces of emerging novel recombinants and their parents in the human population, we isolated mass nucleotide sequence clones of human norovirus genogroups I and II in sewage-affected waters over a 4-year sampling period. Fourteen different phylogenetic combinations of recombinants and their parents were defined from the dozens of phylogenetic lineages circulating in the human population. To evaluate the probability of these combinations, parental lineages of each recombinant were categorized into two groups as HP (relatively higher competitive parents) and LP (relatively lower competitive parents), according to their relative detection frequency. Strong categorization of HP and LP was confirmed by tests with modified data and additional variables. An algorithm that was developed in this study to visualize the chance of mixed infection between parents revealed that HP lineages have a higher chance of mixed infection than LP lineages in the human population. Three parental pairing types in recombinants were defined: HP-HP, HP-LP, and LP-LP. Among these, most recombinants were identified as HP-LP, despite the prediction of dominant emergence of HP-HP type recombinants. These results suggest that nature favors recombinants of human norovirus that originate from parental pairing of heterogeneous competitiveness. IMPORTANCE Novel recombinants, generated from inter- and intra-species recombination of norovirus lineages, often emerge and pose a threat to public health. However, the factors determining emergence of these particular recombinants from all possible combinations of parental lineages remains largely unknown. Therefore, current investigations on these recombinants are inevitably limited to post-epidemic analyses, which merely identify genetic or phenotypic changes in the newly emerged recombinants compared to their parents. Here, we have provided a new theoretical concept that emergence of novel recombinants could be explained by a combination of parental noroviruses thriving in the human population and those circulating at lower levels. This study could provide additional and important rationale for the proactive environmental monitoring of potential future epidemics due to viral recombinants.

Evolutionary Dynamics of Viruses or Microbes, but Not Both

2016 ◽  
Author(s):  
Joshua S. Weitz
Keyword(s):  
Life History ◽  
Evolutionary Dynamics ◽  
Selective Pressure ◽  
Host Interactions ◽  
Intermediate Phenotypes ◽  
Strong Selective Pressure ◽  
Evolution Of Resistance ◽  
Resistance To Infection ◽  
Host Evolution ◽  
Different Levels

This chapter discusses the evolutionary dynamics of viruses. Preexisting variation in host phenotypes include variants with different levels of susceptibility to viruses, including complete resistance. Formative studies of the basis of the mutation rate relied upon virus–host interactions and the possibility of the evolution of resistance to infection. Viruses represent a strong selective pressure and can induce evolution among hosts. Host evolution, as induced by viruses, includes novel forms of ecological dynamics, including cryptic dynamics. Infection of hosts represents a strong selective pressure for viruses. Viruses that differ in their life history traits vary in their fitness and can invade and replace existing viral strains. The latent period represents a model trait for the further study of the evolution of intermediate phenotypes. Evolution among other traits is also possible, including who infects whom.

The catalytic subunit of pseutarin C, a group C prothrombin activator from the venom of Pseudonaja textilis, is structurally similar to mammalian blood coagulation factor Xa

2004 ◽  
Vol 92 (09) ◽  
pp. 509-521 ◽  
Author(s):  
Veena Rao ◽  
Sanjay Swarup ◽  
Manjunatha Kini
Keyword(s):  
Amino Acids ◽  
Factor Xa ◽  
Coagulation Factor ◽  
Catalytic Subunit ◽  
Large Protein ◽  
Heavy Chains ◽  
Large Protein Complex ◽  
Glycosylation Sites ◽  
Mammalian Blood ◽  
Group D

SummaryPseutarin C, a group C prothrombin activator from Pseudonaja textilis venom, is a large protein complex consisting of catalytic and nonenzymatic subunits, which are functionally similar to the mammalian FXa-FVa complex. Here, we present the complete cDNA sequence of the catalytic subunit of pseutarin C. The cDNA of the catalytic subunit encodes a protein of 449 amino acids, which includes a 22-residue signal peptide, 18-residue propeptide and a mature protein of 409 amino acids. The deduced amino acid sequence shows 74-83% identity to group D prothrombin activators from snake venom and ∼42% identity to mammalian FX and has identical domain structure. The precursor of the catalytic subunit of pseutarin C has several unique features. The activation peptide of the catalytic subunit of pseutarin C is significantly smaller (27 as compared to 52 residues in mammalian FX) and does not contain any glycosylation sites. Unlike coagulation FXa, Ser52 and Asn45 of the light and heavy chains are O- and N-glycosylated in pseutarin C catalytic subunit. There is a 12-residue insertion in pseutarin C catalytic subunit close to the region that is implicated in binding to FVa. This is the first sequence of the catalytic subunit of a group C prothrombin activator.

scholarly journals SmartBac, a new baculovirus system for large protein complex production

2019 ◽  
Vol 1 ◽  
pp. 100003 ◽  
Author(s):  
Yujia Zhai ◽  
Danyang Zhang ◽  
Leiye Yu ◽  
Fang Sun ◽  
Fei Sun
Keyword(s):  
Protein Complex ◽  
Large Protein ◽  
Large Protein Complex ◽  
Baculovirus System
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