Independent amylase gene copy number bursts correlate with dietary preferences in mammals

Pajic, Petar; Pavlidis, Pavlos; Dean, Kirsten; Neznanova, Lubov; Romano, Rose‐Anne; Garneau, Danielle; Daugherity, Erin K.; Globig, Anja; Rühl, Stefan; Gökçümen, Ömer

doi:10.7554/elife.44628

Cited by 100 publications

(106 citation statements)

References 75 publications

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“…Copy gain of this gene in C. parapsilosis strains may represent a mechanism for rapid adaptation to fluconazole, the most widely used antifungal in most hospitals (Whaley et al 2016), as a means by which to increase its expression and thus its resistance. Similar gene copy number gains have been reported for the human amylase gene, hypothesized to be in response to increases in starch consumption (Pajic et al 2019). Indeed RTA3 expression in situ from strain C1_006, which has RTA3 in multicopy, was significantly increased as compared to single copy strain CDC317 in culture (Guida et al 2011; Figure 2C).…”

Section: Discussionsupporting

confidence: 78%

Genetic and behavioral adaptation ofCandida parapsilosisto the microbiome of hospitalized infants revealed byin situgenomics, transcriptomics and proteomics

West

Peters

Olm

et al. 2020

Preprint

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Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in microbiome context. Here, we reconstructed five unique C. parapsilosis genomes from premature infant fecal samples and analyzed their genome structure, population diversity and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have four to sixteen copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis coexisted with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition. The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes. DECLARATIONS Ethics approval and consent to participateThis study was reviewed and approved by the University of Pittsburgh Institutional Review Board (IRB PRO12100487 and PRO10090089).

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Section: Discussionsupporting

confidence: 78%

Genetic and behavioral adaptation ofCandida parapsilosisto the microbiome of hospitalized infants revealed byin situgenomics, transcriptomics and proteomics

West

Peters

Olm

et al. 2020

Preprint

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“…Adaptation to starch-rich food has occurred independently in various species via comparable genetic changes, i.e. the duplication of amylase genes in humans, dogs, rats, mice and pigs (Pajic et al, 2019). Other striking examples are the amino-acid replacement mutations M918T and L925I, which, among other sites of the sodium channel gene para (syn.…”

Section: Introductionmentioning

confidence: 99%

The coding loci of evolution and domestication: current knowledge and implications for bio-inspired genome editing

Courtier‐Orgogozo

Martin

2020

Journal of Experimental Biology

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One promising application of CRISPR/Cas9 is to create targeted mutations to introduce traits of interest into domesticated organisms. However, a major current limitation for crop and livestock improvement is to identify the precise genes and genetic changes that must be engineered to obtain traits of interest. Here, we discuss the advantages of bio-inspired genome editing, i.e. the engineered introduction of natural mutations that have already been associated with traits of interest in other lineages (breeds, populations or species). To obtain a landscape view of potential targets for genome editing, we used Gephebase (www.gephebase.org), a manually curated database compiling published data about the genes responsible for evolutionary and domesticated changes across eukaryotes, and examined the >1200 mutations that have been identified in the coding regions of more than 700 genes in animals, plants and yeasts. We observe that our genetic knowledge is relatively important for certain traits, such as xenobiotic resistance, and poor for others. We also note that protein-null alleles, often owing to nonsense and frameshift mutations, represent a large fraction of the known loci of domestication (42% of identified coding mutations), compared with intraspecific (27%) and interspecific evolution (11%). Although this trend may be subject to detection, publication and curation biases, it is consistent with the idea that breeders have selected large-effect mutations underlying adaptive traits in specific settings, but that these mutations and associated phenotypes would not survive the vagaries of changing external and internal environments. Our compilation of the loci of evolution and domestication uncovers interesting options for bio-inspired and transgene-free genome editing.

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“…Variation in the copy number of genes encoding amylase, the enzyme required for breaking down starch, is such an example of convergent evolution. Humans carry extra salivary amylase copies compared to chimpanzees (8,9), owing to high starch consumption that perhaps began before farming (10). Likewise, most dogs, compared to wolves, carry extra pancreatic amylase (AMYB2) copies, possibly facilitating starch digestion in their new environment (11).…”

Section: Perspectivesmentioning

confidence: 99%

Of dogs and men

Pavlidis

Somel

2020

Science

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B ut Argos passed into the darkness of death, now that he had fulfilled his destiny of faith and seen his master once more after twenty years." This quote from The Odyssey vividly illustrates the bond between dog and human. These two species, separated by 90 million years of evolutionary history, have spent much of their recent past in each other's service. This interaction has remodeled both species' environments and has modified the phenotypic and genetic composition of dog populations. On page 557 of this issue, Bergström et al. (1) use 27 ancient dog genomes from across Eurasia, going back 11,000 years, to resolve whether dog domestication happened once or mul

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Independent amylase gene copy number bursts correlate with dietary preferences in mammals

Cited by 100 publications

References 75 publications

Genetic and behavioral adaptation ofCandida parapsilosisto the microbiome of hospitalized infants revealed byin situgenomics, transcriptomics and proteomics

Genetic and behavioral adaptation ofCandida parapsilosisto the microbiome of hospitalized infants revealed byin situgenomics, transcriptomics and proteomics

The coding loci of evolution and domestication: current knowledge and implications for bio-inspired genome editing

Of dogs and men

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