Divergent and parallel routes of biochemical adaptation in high-altitude passerine birds from the Qinghai-Tibet Plateau

When different species experience similar selection pressures, the probability of evolving similar adaptive solutions may be influenced by legacies of evolutionary history, such as lineage-specific changes in genetic background. Here we test for adaptive convergence in hemoglobin (Hb) function among high-altitude passerine birds that are native to the Qinghai-Tibet Plateau, and we examine whether convergent increases in Hb–O2 affinity have a similar molecular basis in different species. We documented that high-altitude parid and aegithalid species from the Qinghai-Tibet Plateau have evolved derived increases in Hb–O2 affinity in comparison with their closest lowland relatives in East Asia. However, convergent increases in Hb–O2 affinity and convergence in underlying functional mechanisms were seldom attributable to the same amino acid substitutions in different species. Using ancestral protein resurrection and site-directed mutagenesis, we experimentally confirmed two cases in which parallel substitutions contributed to convergent increases in Hb–O2 affinity in codistributed high-altitude species. In one case involving the ground tit (Parus humilis) and gray-crested tit (Lophophanes dichrous), parallel amino acid replacements with affinity-enhancing effects were attributable to nonsynonymous substitutions at a CpG dinucleotide, suggesting a possible role for mutation bias in promoting recurrent changes at the same site. Overall, most altitude-related changes in Hb function were caused by divergent amino acid substitutions, and a select few were caused by parallel substitutions that produced similar phenotypic effects on the divergent genetic backgrounds of different species.

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Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1819657116 ◽

2019 ◽

pp. 201819657 ◽

Cited By ~ 1

Author(s):

Yan Hao ◽

Ying Xiong ◽

Yalin Cheng ◽

Gang Song ◽

Chenxi Jia ◽

...

Keyword(s):

Amino Acid ◽

High Altitude ◽

Expression Profiles ◽

Eastern China ◽

Tibet Plateau ◽

Amino Acid Substitutions ◽

Passerine Birds ◽

Specific Expression ◽

Low Altitude ◽

Specific Expression Pattern

High-altitude environments present strong stresses for living organisms, which have driven striking phenotypic and genetic adaptations. While previous studies have revealed multiple genetic adaptations in high-altitude species, how evolutionary history (i.e., phylogenetic background) contributes to similarity in genetic adaptations to high-altitude environments is largely unknown, in particular in a group of birds. We explored this in 3 high-altitude passerine birds from the Qinghai-Tibet Plateau and their low-altitude relatives in lowland eastern China. We generated transcriptomic data for 5 tissues across these species and compared sequence changes and expression shifts between high- and low-altitude pairs. Sequence comparison revealed that similarity in all 3 high-altitude species was high for genes under positive selection (218 genes) but low in amino acid substitutions (only 4 genes sharing identical amino acid substitutions). Expression profiles for all genes identified a tissue-specific expression pattern (i.e., all species clustered by tissue). By contrast, an altitude-related pattern was observed in genes differentially expressed between all 3 species pairs and genes associated with altitude, suggesting that the high-altitude environment may drive similar expression shifts in the 3 high-altitude species. Gene expression level, gene connectivity, and the interactions of these 2 factors with altitude were correlated with evolutionary rates. Our results provide evidence for how gene sequence changes and expression shifts work in a concerted way in a group of high-altitude birds, leading to similar evolution routes in response to high-altitude environmental stresses.

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Identification and genomic characterization of bovine parvovirus 1 in yaks

Journal of Veterinary Diagnostic Investigation ◽

10.1177/10406387211029691 ◽

2021 ◽

pp. 104063872110296

Author(s):

Guoqing Shao ◽

Long Zhao ◽

Cheng Tang ◽

Hua Yue

Keyword(s):

Amino Acid ◽

Tibet Plateau ◽

Molecular Characteristics ◽

Amino Acid Substitutions ◽

Ns1 Protein ◽

Cattle Diseases ◽

Genomic Characterization ◽

Amino Acid Mutations ◽

Bovine Parvovirus ◽

Qinghai Tibet Plateau

Bovine parvovirus 1 (BPV1) is a causative agent of respiratory, gastrointestinal, and reproductive cattle diseases. We collected 149 yak diarrhea fecal samples from 9 farms in the Qinghai-Tibet Plateau. The samples were screened for BPV1 by PCR, and 2 samples were positive for BPV1. The complete genomes of these BPV1 isolates were sequenced successfully. The sequences of these 2 variants were both 5,515 bp in length and shared 96.5–96.8% identity with 2 previously reported BPV1 genomes (GenBank DQ335247, NC_001540). Twenty-six identical amino acid mutations were found in the 2 yak variants, including 7 amino acid substitutions in receptor-binding regions of the VP2 protein, and 5 amino acid substitutions in the NS1 protein C-terminal region that functions to activate transcription. The new genome sequences contribute to better understanding of the evolution and molecular characteristics of BPV1.

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Air–surface exchange of gaseous mercury over permafrost soil: an investigation at a high-altitude (4700 m a.s.l.) and remote site in the central Qinghai-Tibet Plateau

10.5194/acp-2016-515 ◽

2016 ◽

Cited By ~ 1

Author(s):

Zhijia Ci ◽

Fei Peng ◽

Xian Xue ◽

Xiaoshan Zhang

Keyword(s):

High Altitude ◽

Field Experiments ◽

Tibet Plateau ◽

Permafrost Soil ◽

Remote Site ◽

Water Addition ◽

Surface Exchange ◽

Entire Study ◽

Gaseous Mercury ◽

Qinghai Tibet Plateau

Abstract. The pattern of air–surface gaseous mercury (mainly Hg(0)) exchange in the Qinghai-Tibet Plateau (QTP) may be unique because this region is characterized by low temperature, great temperature variation, intensive solar radiation, and pronounced freeze-thaw process of permafrost soils. However, air–surface Hg(0) flux in the QTP is poorly investigated. In this study, we performed filed measurements and controlled field experiments with dynamic flux chambers technique to examine the flux, temporal variation and influencing factors of air–surface Hg(0) exchange at a high-altitude (4700 m a.s.l.) and remote site in the central QTP. The results of field measurements showed that surface soils were net emission source of Hg(0) in the entire study. Hg(0) flux showed remarkable seasonality with net high emission in the warm campaigns and net low deposition in winter campaign, and also showed the diurnal pattern with emission in daytime and deposition in nighttime, especially on days without precipitation. Rainfall events on the dry soils induced large and immediate increase in Hg(0) emission. Snowfall events did not induce the pulse of Hg(0) emission, but snow melt resulted in the immediate increase in Hg(0) emission. Daily Hg(0) fluxes on rainy or snowy days were higher than those of days without precipitation. Controlled field experiments suggested that water addition to dry soils significantly increased Hg(0) emission both in short and relatively long timescales, and also showed that UV radiation was primarily attributed to Hg(0) emission in the daytime. Our findings imply that a warm climate and environmental change could facilitate Hg release from the permafrost terrestrial ecosystem in the QTP.

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Comparing mutagenesis and simulations as tools for identifying functionally important sequence changes for protein thermal adaptation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1817455116 ◽

2018 ◽

Vol 116 (2) ◽

pp. 679-688 ◽

Cited By ~ 12

Author(s):

Ming-ling Liao ◽

George N. Somero ◽

Yun-wei Dong

Keyword(s):

Amino Acid ◽

Thermal Adaptation ◽

Site Directed Mutagenesis ◽

Dynamics Simulation ◽

Amino Acid Substitutions ◽

Thermal Stabilities ◽

Specific Amino Acid ◽

Enzyme Thermal Stability ◽

And Function

Comparative studies of orthologous proteins of species evolved at different temperatures have revealed consistent patterns of temperature-related variation in thermal stabilities of structure and function. However, the precise mechanisms by which interspecific variations in sequence foster these adaptive changes remain largely unknown. Here, we compare orthologs of cytosolic malate dehydrogenase (cMDH) from marine molluscs adapted to temperatures ranging from −1.9 °C (Antarctica) to ∼55 °C (South China coast) and show how amino acid usage in different regions of the enzyme (surface, intermediate depth, and protein core) varies with adaptation temperature. This eukaryotic enzyme follows some but not all of the rules established in comparisons of archaeal and bacterial proteins. To link the effects of specific amino acid substitutions with adaptive variations in enzyme thermal stability, we combined site-directed mutagenesis (SDM) and in vitro protein experimentation with in silico mutagenesis using molecular dynamics simulation (MDS) techniques. SDM and MDS methods generally but not invariably yielded common effects on protein stability. MDS analysis is shown to provide insights into how specific amino acid substitutions affect the conformational flexibilities of mobile regions (MRs) of the enzyme that are essential for binding and catalysis. Whereas these substitutions invariably lie outside of the MRs, they effectively transmit their flexibility-modulating effects to the MRs through linked interactions among surface residues. This discovery illustrates that regions of the protein surface lying outside of the site of catalysis can help establish an enzyme’s thermal responses and foster evolutionary adaptation of function.

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Supplementary material to "Air–surface exchange of gaseous mercury over permafrost soil: an investigation at a high-altitude (4700 m a.s.l.) and remote site in the central Qinghai-Tibet Plateau"

10.5194/acp-2016-515-supplement ◽

2016 ◽

Author(s):

Zhijia Ci ◽

Fei Peng ◽

Xian Xue ◽

Xiaoshan Zhang

Keyword(s):

High Altitude ◽

Tibet Plateau ◽

Permafrost Soil ◽

Remote Site ◽

Surface Exchange ◽

Gaseous Mercury ◽

Supplementary Material ◽

Qinghai Tibet Plateau

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Functional effects of single amino acid substitutions in the region of Phe113 to Asp138 in the plasminogen activator inhibitor 1 molecule

Biochemical Journal ◽

10.1042/bj3310409 ◽

1998 ◽

Vol 331 (2) ◽

pp. 409-415 ◽

Cited By ~ 15

Author(s):

Guang-Chao SUI ◽

Björn WIMAN

Keyword(s):

Amino Acid ◽

Plasminogen Activator ◽

Plasminogen Activator Inhibitor ◽

Site Directed Mutagenesis ◽

Single Amino Acid ◽

Amino Acid Substitutions ◽

Plasminogen Activator Inhibitor 1 ◽

Low Activity ◽

Activator Inhibitor ◽

Pai 1

Thirteen amino acid substitutions have been introduced within the stretch Phe113 to Asp138 in the plasminogen activator inhibitor 1 (PAI-1) molecule by site-directed mutagenesis. The different proteins and wild-type (wt) PAI-1 have been overexpressed in Escherichia coliand purified by chromatography on heparin–Sepharose and on anhydrotrypsin–agarose. The PAI-1 variants have been characterized by their reactivity with tissue plasminogen activator (tPA), interactions with vitronectin or heparin, and stability. Most PAI-1 variants, except for Asp125 → Lys, Phe126 → Ser and Arg133 → Asp, displayed a high spontaneous inhibitory activity towards tPA, which did not change greatly on reactivation with 4 M guanidinium chloride, followed by dialysis at pH 5.5. The variants Asp125 → Lys and Arg133 → Asp became much more active after reactivation and they were also more rapidly transformed to inactive forms (t½ 22–31 min) at physiological pH and temperature than the other variants. However, in the presence of vitronectin they were both almost equally stable (t½ 2.3 h) as wtPAI-1 (t½ 3.0 h). The mutant Glu130 → Lys showed an increased stability, both in the absence and in the presence of vitronectin compared with wtPAI-1. Nevertheless a similar affinity between all the active PAI-1 variants and vitronectin was observed. Further, all mutants, including the three mutants with low activity, were to a large extent adsorbed on anhydrotrypsin–agarose and were eluted in a similar fashion. In accordance with these data, the three variants with a low activity were all to a large extent cleaved as a result of their reaction with tPA, suggesting that they occurred predominantly in the substrate conformation. Our results do not support the presence of a binding site for vitronectin in this part of the molecule, but rather that it might be involved in controlling the active PAI-1 to substrate transition. Partly, this region of the PAI-1 molecule (Arg115 to Arg118) seems also to be involved in the binding of heparin to PAI-1.

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Resolving the energy restriction at high altitude: variation in the digestive system of Phrynocephalus vlangalii

Animal Biology ◽

10.1163/15707563-bja10004 ◽

2020 ◽

Vol 70 (3) ◽

pp. 321-331

Author(s):

Yang yang Zhao ◽

Yue Qi ◽

Xiao ning Wang ◽

Wei Zhao

Keyword(s):

High Altitude ◽

Digestive Tract ◽

Native Species ◽

Morphological Structure ◽

Histological Change ◽

Energy Restriction ◽

Tibet Plateau ◽

Argyrophil Cells ◽

Energy Limitation ◽

Qinghai Tibet Plateau

Abstract Hypothermic and hypoxic environments create strong selective pressure on native species by affecting, among other things, the relationship between energy intake and allocation. In order to detect the adaptation of Phrynocephalus vlangalii to such energy limitation, the morphological structure and argyrophil cells of the digestive tract of 80 individuals from two different altitudes in the Qinghai-Tibet Plateau were compared using overall anatomy as well as paraffin sectioning of specific organs. Compared with the low-altitude population, the high-altitude individuals were found to have a significantly longer stomach and duodenum, longer and wider villus in the small intestine, larger surface area in duodenum and jejunum, and more argyrophilic cells in stomach and duodenum. Our results indicate that the morphological and histological change of the digestive tract may be conductive to the plateau adaptability of P. vlangalii by enhancing the efficiency of digestion and absorption. For a more general conclusion to be drawn, comparison of more populations at both altitudes is required in addition to verifying how phenotypically flexible these traits are.

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