scholarly journals Variation in selection constraints on teleost TLRs with emphasis on their repertoire in the Walking catfish, Clarias batrachus

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Manisha Priyam ◽  
Sanjay K. Gupta ◽  
Biplab Sarkar ◽  
T. R. Sharma ◽  
A. Pattanayak
Keyword(s):  
Phylogenetic Analysis ◽  
Positive Selection ◽  
Strong Evidence ◽  
Selection Pressure ◽  
Arms Race ◽  
Clarias Batrachus ◽  
Toll Like Receptors ◽  
Specific Variation ◽  
Species Specific ◽  
High Degree

AbstractThe high degree of conservation of toll-like receptors (TLRs), and yet their subtle variations for better adaptation of species in the host–pathogen arms race make them worthy candidates for understanding evolution. We have attempted to track the trend of TLR evolution in the most diverse vertebrate group—teleosts, where Clarias batrachus was given emphasis, considering its traits for terrestrial adaptation. Eleven C. batrachus TLRs (TLR1, 2, 3, 5, 7, 8 9, 13, 22, 25, 26) were identified in this study which clustered in proximity to its Siluriformes relative orthologues in the phylogenetic analysis of 228 TLRs from 25 teleosts. Ten TLRs (TLR1, 2, 3, 5, 7, 8 9, 13, 21, 22) with at least 15 member orthologues for each alignment were processed for selection pressure and coevolutionary analysis. TLR1, 7, 8 and 9 were found to be under positive selection in the alignment-wide test. TLR1 also showed maximum episodic diversification in its clades while the teleost group Eupercaria showed the maximum divergence in their TLR repertoire. Episodic diversification was evident in C. batrachus TLR1 and 7 alignments. These results present a strong evidence of a divergent TLR repertoire in teleosts which may be contributing towards species-specific variation in TLR functions.

scholarly journals Correction to: Ultraviolet absorbance of Sphagnum magellanicum, S. fallax and S. fuscum extracts with seasonal and species‑specific variation

2021 ◽  
Vol 20 (4) ◽  
pp. 597-598
Author(s):  
J. Tienaho ◽  
N. Silvan ◽  
R. Muilu-Mäkelä ◽  
P. Kilpeläinen ◽  
E. Poikulainen ◽  
...  
Keyword(s):  
Ultraviolet Absorbance ◽  
Specific Variation ◽  
Species Specific ◽  
Sphagnum Magellanicum

scholarly journals A Single Adaptive Mutation in Sodium Taurocholate Cotransporting Polypeptide Induced by Hepadnaviruses Determines Virus Species Specificity

2018 ◽  
Vol 93 (5) ◽  
Author(s):  
Junko S. Takeuchi ◽  
Kento Fukano ◽  
Masashi Iwamoto ◽  
Senko Tsukuda ◽  
Ryosuke Suzuki ◽  
...  
Keyword(s):  
Amino Acid ◽  
Virus Infection ◽  
Positive Selection ◽  
Sodium Taurocholate ◽  
Arms Race ◽  
Adaptive Mutation ◽  
Molecular Evidence ◽  
Adaptive Mutations ◽  
Wide Range ◽  
Coevolutionary Arms Race

ABSTRACTHepatitis B virus (HBV) and its hepadnavirus relatives infect a wide range of vertebrates, from fish to human. Hepadnaviruses and their hosts have a long history of acquiring adaptive mutations. However, there are no reports providing direct molecular evidence for such a coevolutionary “arms race” between hepadnaviruses and their hosts. Here, we present evidence suggesting that the adaptive evolution of the sodium taurocholate cotransporting polypeptide (NTCP), an HBV receptor, has been influenced by virus infection. Evolutionary analysis of the NTCP-encoding genes from 20 mammals showed that most NTCP residues are highly conserved among species, exhibiting evolution under negative selection (dN/dSratio [ratio of nonsynonymous to synonymous evolutionary changes] of <1); this observation implies that the evolution of NTCP is restricted by maintaining its original protein function. However, 0.7% of NTCP amino acid residues exhibit rapid evolution under positive selection (dN/dSratio of >1). Notably, a substitution at amino acid (aa) 158, a positively selected residue, converting the human NTCP to a monkey-type sequence abrogated the capacity to support HBV infection; conversely, a substitution at this residue converting the monkey Ntcp to the human sequence was sufficient to confer HBV susceptibility. Together, these observations suggested a close association of the aa 158 positive selection with the pressure by virus infection. Moreover, the aa 158 sequence determined attachment of the HBV envelope protein to the host cell, demonstrating the mechanism whereby HBV infection would create positive selection at this NTCP residue. In summary, we provide the first evidence in agreement with the function of hepadnavirus as a driver for inducing adaptive mutation in host receptor.IMPORTANCEHBV and its hepadnavirus relatives infect a wide range of vertebrates, with a long infectious history (hundreds of millions of years). Such a long history generally allows adaptive mutations in hosts to escape from infection while simultaneously allowing adaptive mutations in viruses to overcome host barriers. However, there is no published molecular evidence for such a coevolutionary arms race between hepadnaviruses and hosts. In the present study, we performed coevolutionary phylogenetic analysis between hepadnaviruses and the sodium taurocholate cotransporting polypeptide (NTCP), an HBV receptor, combined with virological experimental assays for investigating the biological significance of NTCP sequence variation. Our data provide the first molecular evidence supporting that HBV-related hepadnaviruses drive adaptive evolution in the NTCP sequence, including a mechanistic explanation of how NTCP mutations determine host viral susceptibility. Our novel insights enhance our understanding of how hepadnaviruses evolved with their hosts, permitting the acquisition of strong species specificity.

scholarly journals Loss of Heterozygosity and Base Mutation Rates Vary Among Saccharomyces cerevisiae Hybrid Strains

2020 ◽  
Vol 10 (9) ◽  
pp. 3309-3319 ◽  
Author(s):  
Ajith V Pankajam ◽  
Suman Dash ◽  
Asma Saifudeen ◽  
Abhishek Dutta ◽  
Koodali T Nishant
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Loss Of Heterozygosity ◽  
Mutation Rates ◽  
Single Nucleotide ◽  
Single Nucleotide Mutation ◽  
Genome Wide ◽  
Nucleotide Mutation ◽  
Specific Variation ◽  
Chromosomal Changes ◽  
Species Specific

Abstract A growing body of evidence suggests that mutation rates exhibit intra-species specific variation. We estimated genome-wide loss of heterozygosity (LOH), gross chromosomal changes, and single nucleotide mutation rates to determine intra-species specific differences in hybrid and homozygous strains of Saccharomyces cerevisiae. The mutation accumulation lines of the S. cerevisiae hybrid backgrounds - S288c/YJM789 (S/Y) and S288c/RM11-1a (S/R) were analyzed along with the homozygous diploids RM11, S288c, and YJM145. LOH was extensive in both S/Y and S/R hybrid backgrounds. The S/Y background also showed longer LOH tracts, gross chromosomal changes, and aneuploidy. Short copy number aberrations were observed in the S/R background. LOH data from the S/Y and S/R hybrids were used to construct a LOH map for S288c to identify hotspots. Further, we observe up to a sixfold difference in single nucleotide mutation rates among the S. cerevisiae S/Y and S/R genetic backgrounds. Our results demonstrate LOH is common during mitotic divisions in S. cerevisiae hybrids and also highlight genome-wide differences in LOH patterns and rates of single nucleotide mutations between commonly used S. cerevisiae hybrid genetic backgrounds.

scholarly journals Odorant receptor copy number change, co-expression, and positive selection establish peripheral coding differences between fly species

2021 ◽  
Author(s):  
Thomas O. Auer ◽  
Raquel Álvarez-Ocaña ◽  
Steeve Cruchet ◽  
Richard Benton ◽  
J. Roman Arguello
Keyword(s):  
Positive Selection ◽  
Sensory Neuron ◽  
Copy Number ◽  
Odorant Receptor ◽  
Chemosensory Receptor ◽  
Large Gene ◽  
Neuron Populations ◽  
Copy Number Changes ◽  
Species Specific

Animals sample their chemical environment using sensory neurons that express diverse chemosensory receptors, which trigger responses when they bind environmental molecules. In addition to modifications in the ligand binding properties of receptors, chemosensory receptor evolution is characterized by copy number changes, often resulting in large gene family size differences between species. Though chemosensory receptor expansions and contractions are frequently described, it is unknown how this is accompanied by changes in the neural circuitry in which they are expressed. Among Drosophila's chemosensory receptor families, the Odorant receptors (Ors) are ideal for addressing this question because, other than an essential co-receptor (Orco), a large majority of Ors are uniquely expressed in single olfactory sensory neuron (OSN) populations. Between-species changes in Or copy number, therefore, may indicate diversification or reduction of peripheral sensory neuron populations. To test this possibility, we focused on a rapidly duplicated/deleted Or subfamily - named Or67a - within Drosophila melanogaster and its most closely-related sister species (D. simulans, D. sechellia, and D. mauritiana). Evolutionary genetic analyses and in vivo physiological assays demonstrate that the common ancestor of these four species possessed three Or67a paralogs that had already diverged adaptively in their odor-evoked responses. Following the group's speciation events, two Or67a paralogs were independently lost in D. melanogaster and D. sechellia, with positive selection continuing to act on the intact genes. Instead of the expected singular expression of each of the functionally diverged Ors in different neurons, we found that the three D. simulans Or67a paralogs are co-expressed in the same cells. Thus, while neuroanatomy is conserved between these species, independent selection on co-expressed receptors has contributed to species-specific peripheral coding of olfactory information. This work reveals a model of adaptive change previously not considered for olfactory evolution and raises the possibility that similar processes may be operating among the largely uninvestigated cases of Or co-expression.

scholarly journals Structure, expression and phylogenetic analysis of the gene encoding actin I in Pneumocystis carinii.

Genetics ◽  
1994 ◽  
Vol 137 (3) ◽  
pp. 743-750 ◽  
Author(s):  
L D Fletcher ◽  
J M McDowell ◽  
R R Tidwell ◽  
R B Meagher ◽  
C C Dykstra
Keyword(s):  
Phylogenetic Analysis ◽  
Essential Gene ◽  
Pneumocystis Carinii ◽  
Comparative Sequence Analysis ◽  
Cdna Clones ◽  
Actin Gene ◽  
Gene Encoding ◽  
Actin Protein ◽  
Relationship Of ◽  
High Degree

Abstract Actin is a major component of the cytoskeleton and one of the most abundant proteins found in eukaryotic cells. Comparative sequence analysis shows that this essential gene has been highly conserved throughout eukaryotic evolution making it useful for phylogenetic analysis. Complete cDNA clones for the actin-encoding gene were isolated and characterized from Pneumocystis carinii purified from immunosuppressed rat lungs. The nucleotide sequence encodes a protein of 376 amino acids. The predicted actin protein of P. carinii shares a high degree of conservation to other known actins. Only one major actin gene was found in P. carinii. The P. carinii actin sequence was compared with 30 other actin sequences. Gene phylogenies constructed using both neighbor-joining and protein parsimony methods places the P. carinii actin sequence closest to the majority of the fungi. Since the phylogenetic relationship of P. carinii to fungi and protists has been questioned, these data on the actin gene phylogeny support the grouping of P. carinii with the fungi.

scholarly journals Smc5/6-antagonism by HBx is an evolutionary-conserved function of hepatitis B virus infection in mammals

2017 ◽  
Author(s):  
Fabien Filleton ◽  
Fabien Abdul ◽  
Laetitia Gerossier ◽  
Alexia Paturel ◽  
Janet Hall ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Antiviral Activity ◽  
Positive Selection ◽  
Host Species ◽  
Human Hepatocytes ◽  
Arms Race ◽  
Restriction Factor ◽  
Primary Human Hepatocytes ◽  
B Virus

AbstractInfection with Hepatitis B virus (HBV) is a major cause of liver disease and cancer in humans. HBVs (family Hepadnaviridae) have been associated with mammals for millions of years. Recently, the Smc5/6 complex, known for its essential housekeeping functions in genome maintenance, was identified as an antiviral restriction factor of human HBV. The virus has however developed a counteraction mechanism by degrading the complex via its regulatory HBx protein. Whether the antiviral activity of the Smc5/6 complex against hepadnaviruses is an important and evolutionary-conserved function is unknown. Here, we used a combined evolutionary and functional approach to address this question. We first performed phylogenetic and positive selection analyses of the six Smc5/6 complex subunits and found that they have been highly conserved in primates and mammals. Yet, the Smc6 subunit showed marks of adaptive evolution, potentially reminiscent of virus-host “arms-race” We then functionally tested the HBx from six very divergent hepadnaviruses now naturally infecting primates, rodents, and bats. Despite little sequence homology, we demonstrate that these HBx efficiently degraded mammalian Smc5/6 complexes, independently of the host species and of the sites under positive selection. Importantly, all also rescued the replication of an HBx-deficient HBV in primary human hepatocytes. These findings point to an evolutionary-conserved requirement for Smc5/6 inactivation by HBx, showing that the Smc5/6 antiviral activity has been an important defense mechanism against hepadnaviruses in mammals. Interestingly, Smc5/6 may further be a restriction factor of other yet unidentified viruses that have driven some of its adaptation.ImportanceInfection with hepatitis B virus (HBV) led to 887000 human deaths in 2015. HBV has been co-evolving with mammals for millions of years. Recently, the Smc5/6 complex, known for its essential housekeeping functions, was identified as a restriction factor of human HBV antagonized by the regulatory HBx protein. Here, we address whether the antiviral activity of Smc5/6 is an important evolutionary-conserved function. We found that all six subunits of Smc5/6 have been conserved in primates with only Smc6 showing signatures of “evolutionary arms-race” Using evolutionary-guided functional assays that include infections of primary human hepatocytes, we demonstrate that HBx from very divergent mammalian HBVs could all efficiently antagonize Smc5/6, independently of the host species and sites under positive selection. These findings show that the Smc5/6 antiviral activity against HBV is an important function in mammals. It also raises the intriguing possibility that Smc5/6 restricts other, yet unidentified viruses.

scholarly journals Monkeying around with venom: an increased resistance to α-neurotoxins supports an evolutionary arms race between Afro-Asian primates and sympatric cobras

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Richard J. Harris ◽  
K. Anne-Isola Nekaris ◽  
Bryan G. Fry
Keyword(s):  
Nicotinic Acetylcholine Receptors ◽  
Acetylcholine Receptors ◽  
Selection Pressure ◽  
Arms Race ◽  
Last Common Ancestor ◽  
Geographic Ranges ◽  
Venomous Snakes ◽  
Snake Detection ◽  
Coevolutionary Arms Race

Abstract Background Snakes and primates have a multi-layered coevolutionary history as predators, prey, and competitors with each other. Previous work has explored the Snake Detection Theory (SDT), which focuses on the role of snakes as predators of primates and argues that snakes have exerted a selection pressure for the origin of primates’ visual systems, a trait that sets primates apart from other mammals. However, primates also attack and kill snakes and so snakes must simultaneously avoid primates. This factor has been recently highlighted in regard to the movement of hominins into new geographic ranges potentially exerting a selection pressure leading to the evolution of spitting in cobras on three independent occasions. Results Here, we provide further evidence of coevolution between primates and snakes, whereby through frequent encounters and reciprocal antagonism with large, diurnally active neurotoxic elapid snakes, Afro-Asian primates have evolved an increased resistance to α-neurotoxins, which are toxins that target the nicotinic acetylcholine receptors. In contrast, such resistance is not found in Lemuriformes in Madagascar, where venomous snakes are absent, or in Platyrrhini in the Americas, where encounters with neurotoxic elapids are unlikely since they are relatively small, fossorial, and nocturnal. Within the Afro-Asian primates, the increased resistance toward the neurotoxins was significantly amplified in the last common ancestor of chimpanzees, gorillas, and humans (clade Homininae). Comparative testing of venoms from Afro-Asian and American elapid snakes revealed an increase in α-neurotoxin resistance across Afro-Asian primates, which was likely selected against cobra venoms. Through structure-activity studies using native and mutant mimotopes of the α-1 nAChR receptor orthosteric site (loop C), we identified the specific amino acids responsible for conferring this increased level of resistance in hominine primates to the α-neurotoxins in cobra venom. Conclusion We have discovered a pattern of primate susceptibility toward α-neurotoxins that supports the theory of a reciprocal coevolutionary arms-race between venomous snakes and primates.

Spatio-temporal and species-specific variation in PBDE levels/patterns in British Columbia's coastal waters

2006 ◽  
Vol 140 (2) ◽  
pp. 355-363 ◽  
Author(s):  
Michael G. Ikonomou ◽  
Marc P. Fernandez ◽  
Zachary L. Hickman
Keyword(s):  
Coastal Waters ◽  
Specific Variation ◽  
Spatio Temporal ◽  
Species Specific
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