Signatures of relaxed selection in the <i>CYP8B1</i> gene of birds and mammals

Shinde, Sagar Sharad; Teekas, Lokdeep; Sharma, Sandhya; Vijay, Nagarjun

doi:10.1101/714188

Cited by 4 publications

(5 citation statements)

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“…These differences in the inferences based on the multiple sequence aligner used are known to occur when the sequences are highly diverged ( Blackburne & Whelan, 2013 ). I have shown earlier that genes can experience relaxed selection when the c-terminal end is increased in length due to change in the position of the stop codon ( Shinde et al, 2019 ). Hence, the relaxed selection detected in the CENPA/CSE4 gene could simply be a result of drastic change in the length of the n-terminal sequence.…”

Section: Resultsmentioning

confidence: 99%

Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast

Vijay

2020

PeerJ

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Background The genomic sequences of centromeres, as well as the set of proteins that recognize and interact with centromeres, are known to quickly diverge between lineages potentially contributing to post-zygotic reproductive isolation. However, the actual sequence of events and processes involved in the divergence of the kinetochore machinery is not known. The patterns of gene loss that occur during evolution concomitant with phenotypic changes have been used to understand the timing and order of molecular changes. Methods I screened the high-quality genomes of twenty budding yeast species for the presence of well-studied kinetochore genes. Based on the conserved gene order and complete genome assemblies, I identified gene loss events. Subsequently, I searched the intergenic regions to identify any un-annotated genes or gene remnants to obtain additional evidence of gene loss. Results My analysis identified the loss of four genes (NKP1, NKP2, CENPL/IML3 and CENPN/CHL4) of the inner kinetochore constitutive centromere-associated network (CCAN/also known as CTF19 complex in yeast) in both the Naumovozyma species for which genome assemblies are available. Surprisingly, this collective loss of four genes of the CCAN/CTF19 complex coincides with the emergence of unconventional centromeres in N. castellii and N. dairenensis. My study suggests a tentative link between the emergence of unconventional point centromeres and the turnover of kinetochore genes in budding yeast.

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Section: Resultsmentioning

confidence: 99%

Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast

Vijay

2020

PeerJ

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“…In primate species, the potential addition of the extra coding-exon occurs by a shift of the start codon into the untranslated region. Such changes at the reading frame termini occur when the gene is under relaxed selective constraints (Shinde et al, 2019). Acquisition of novel protein-coding sequences through changes in the exon length is also known to occur (Kishida et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…Molecular signatures of relaxation in the degree of purifying selection generally accompany the loss of gene functionality and have been used as evidence of gene loss (Hecker et al, 2017; Sharma and Hiller, 2018; Shinde et al, 2019). Based on the gene sequence of COA1/MITRAC15 , we could identify eleven Galliform species with gene-disrupting mutations (see Supplementary Table S8 and S9 ).…”

Section: Methodsmentioning

confidence: 99%

Recurrent erosion ofCOA1/MITRAC15demonstrates gene dispensability in oxidative phosphorylation

Sharma

Teekas

et al. 2021

Preprint

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Skeletal muscle fibers rely upon either oxidative phosphorylation or glycolytic pathway to achieve muscular contractions that power mechanical movements. Species with energy-intensive adaptive traits that require sudden bursts of energy have a greater dependency on fibers that use the glycolytic pathway. Glycolytic fibers have decreased reliance on OXPHOS and lower mitochondrial content compared to oxidative fibers. Hence, we hypothesized that adaptive gene loss might have occurred within the OXPHOS pathway in lineages that largely depend on glycolytic fibers. The protein encoded by the COA1/MITRAC15 gene with conserved orthologs found in budding yeast to humans promotes mitochondrial translation. We show that gene disrupting mutations have accumulated within the COA1/MITRAC15 gene in the cheetah, several species of galliforms, and rodents. The genomic region containing COA1/MITRAC15 is a well-established evolutionary breakpoint region in mammals. Careful inspection of genome assemblies of closely related species of rodents and marsupials suggests two independent COA1/MITRAC15 gene loss events co-occurring with chromosomal rearrangements. Besides recurrent gene loss events, we document changes in COA1/MITRAC15 exon structure in primates and felids. The detailed evolutionary history presented in this study reveals the intricate link between skeletal muscle fiber composition and dispensability of the chaperone-like role of the COA1/MITRAC15 gene.

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“…The manually curated open reading frame multi-fasta files consisting of 70 genes from ~15 primate species were collected from Ensembl. We extend our previous multiple sequence alignment strategy(53) by including additional multiple sequence alignment programs to generate 8 independent alignments for each gene. Several multiple sequence alignment tools were used to ensure that the inferred patterns of sequence evolution are not restricted to the alignment strategy used.…”

Section: Methodsmentioning

confidence: 99%

Coevolution of retroviruses withSERINCs following whole-genome duplication divergence

Ramdas

Bhardwaj

Singh

et al. 2020

Preprint

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9The SERINC gene family comprises of five paralogs in humans of which SERINC3 and 10 SERINC5 inhibit HIV-1 infectivity and are counteracted by Nef. The origin of this anti-retroviral 11 activity, its prevalence among the remaining human paralogs, and its ability to target 12 retroviruses remain largely unknown. Here we show that despite their early divergence, the 13 anti-retroviral activity is functionally conserved among four human SERINC paralogs with 14 SERINC2 being an exception. The lack of activity in human SERINC2 is associated with its 15 post-whole genome duplication (WGD) divergence, as evidenced by the ability of pre-WGD 16 orthologs from yeast, fly, and a post-WGD-proximate SERINC2 from coelacanth to inhibit nef-17 defective HIV-1. Intriguingly, potent retroviral factors from HIV-1 and MLV are not able to relieve 18 the SERINC2-mediated particle infectivity inhibition, indicating that such activity was directed 19 towards other retroviruses that are found in coelacanth (like foamy viruses). However, foamy-20 derived vectors are intrinsically resistant to the action of SERINC2, and we show that a foamy 21 virus envelope confers this resistance. Despite the presence of weak arms-race signatures, the 22 functional reciprocal adaptation among SERINC2 and SERINC5 and, in response, the 23 emergence of antagonizing ability in foamy virus appears to have resulted from a long-term 24 conflict with the host. 25 26 27 28 Introduction 29Viruses have been exploiting the host machinery for their persistence, and, in response, the 30 host has continued to evolve increasingly intricate antiviral defense strategies. As part of this 31 ongoing arms-race, while viruses have relied on acquisition and fusion of diverse genes (1), 32 the host-defense mechanism has been made possible by the functional divergence of gene 33 copies following duplication of genes as well as whole-genomes (2-7). Restriction factors being 34 at the forefront of this long-term conflict (8-10), show clear molecular signatures of arms-race 35 (11,12). In fact, the presence of these signatures has been proposed to be a hallmark of 36 restriction factors (8,13), and has been used as a screening strategy to identify potential 37 candidates (2,14). In contrast, the recently identified anti-retroviral host inhibitors SERINC5 and 38 SERINC3 display an uneventful evolutionary history (15). This is counterintuitive, because 39 distant retroviruses, with wide host-range, encode anti-SERINC5 virulent factors (16)(17)(18). We, 40Ramdas et al.therefore, sought to trace the origins of this antiretroviral activity and its relevance for retroviral 41 inhibition. Our analysis to comprehend the evolutionary origins of the antiretroviral activity in 42 SERINCs, identifies an active SERINC2 with a hitherto unknown interaction with a foamy virus. 44 Results 45Antiretroviral activity among human SERINC paralogs 46 Analysis of sequence similarity and gene structure conservation reveals that SERINC5 and 47 SERINC4 share a recent ancestry (Fig-S1). Similarly, SERINC3 and...

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Signatures of relaxed selection in the CYP8B1 gene of birds and mammals

Cited by 4 publications

References 66 publications

Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast

Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast

Recurrent erosion ofCOA1/MITRAC15demonstrates gene dispensability in oxidative phosphorylation

Coevolution of retroviruses withSERINCs following whole-genome duplication divergence

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