The fitness challenge of studying molecular adaptation

Advances in bioinformatics and high-throughput genetic analysis increasingly allow us to predict the genetic basis of adaptive traits. These predictions can be tested and confirmed, but the molecular-level changes - i.e. the molecular adaptation - that link genetic differences to organism fitness remain generally unknown. In recent years, a series of studies have started to unpick the mechanisms of adaptation at the molecular level. In particular, this work has examined how changes in protein function, activity, and regulation cause improved organismal fitness. Key to addressing molecular adaptations is identifying systems and designing experiments that integrate changes in the genome, protein chemistry (molecular phenotype), and fitness. Knowledge of the molecular changes underpinning adaptations allow new insight into the constraints on, and repeatability of adaptations, and of the basis of non-additive interactions between adaptive mutations. Here we critically discuss a series of studies that examine the molecular-level adaptations that connect genetic changes and fitness.

Allosteric mechanisms underlying the adaptive increase in hemoglobin-oxygen affinity of the bar-headed goose

The high blood-O2 affinity of the bar-headed goose (Anser indicus) is an integral component of the biochemical and physiological adaptations that allow this hypoxia-tolerant species to undertake migratory flights over the Himalayas. The high blood-O2 affinity of this species was originally attributed to a single amino acid substitution of the major hemoglobin (Hb) isoform, HbA, which was thought to destabilize the low-affinity T state, thereby shifting the T-R allosteric equilibrium towards the high-affinity R state. Surprisingly, this mechanistic hypothesis has never been addressed using native proteins purified from blood. Here, we report a detailed analysis of O2 equilibria and kinetics of native major HbA and minor HbD isoforms from bar-headed goose and greylag goose (Anser anser), a strictly lowland species, to identify and characterize the mechanistic basis for the adaptive change in Hb function. We find that HbA and HbD of bar-headed goose have consistently higher O2 affinities than those of the greylag goose. The corresponding Hb isoforms of the two species are equally responsive to physiological allosteric cofactors and have similar Bohr effects. Thermodynamic analyses of O2 equilibrium curves according to the two-state Monod-Wyman-Changeaux model revealed higher R-state O2 affinities in the bar-headed goose Hbs, associated with lower O2 dissociation rates, compared with the greylag goose. Conversely, the T state was not destabilized and the T-R allosteric equilibrium was unaltered in bar-headed goose Hbs. The physiological implication of these results is that increased R-state affinity allows for enhanced O2 saturation in the lungs during hypoxia, but without impairing O2 delivery to tissues.

Molecular basis of bird respiration: primary hemoglobin structure component from Tufted duck (Aythya fuligula, Anseriformes)--role of alpha99Arg in formation of a complex salt bridge network

The primary structure of the major hemoglobin component, HbA (alpha(A)- and beta-chain), from Tufted duck (Aythya fuligula) is presented. The separation of the globin subunits was achieved by ion exchange chromatography on CM-cellulose in 8 M urea. The amino acid sequence was determined by automatic Edman degradation of native chains as well as tryptic and hydrolytic peptides in a gas-phase sequencer. The automated homology model was generated by the protein structure modeling package WHAT IF using the crystal structure coordinates of Bar-headed goose hemoglobin. The 3D structure prediction enables alpha99Arg and beta101Glu to emerge as a new intersubunit contact site not found in the hemoglobin structure of any other species. alpha99Arg forms a complex salt bridge network involving alpha99Arg-beta101Glu-beta104Arg-beta108Asp. Also the substitution at alpha34 --> Ile, alpha38 --> Gln and beta55 --> Leu serves to stabilize the oxy-structure, leading to higher oxygen affinity.

The crystal structure of bar-headed goose hemoglobin in deoxy form: the allosteric mechanism of a hemoglobin species with high oxygen affinity

The crystal structure of a high oxygen affinity species of hemoglobin, bar-headed goose hemoglobin in deoxy form, has been determined to a resolution of 2.8 A. The R and R(free) factor of the model are 0.197 and 0.243, respectively. The structure reported here is a special deoxy state of hemoglobin and indicates the differences in allosteric mechanisms between the goose and human hemoglobins. The quaternary structure of the goose deoxy hemoglobin shows obvious differences from that of human deoxy hemoglobin. The rotation angle of one alphabeta dimer relative to its partner in a tetramer molecule from the goose oxy to deoxy hemoglobin is only 4.6 degrees, and the translation is only 0.3 A, which are much smaller than those in human hemoglobin. In the alpha(1)beta(2) switch region of the goose deoxy hemoglobin, the imidazole ring of His beta(2)97 does not span the side-chain of Thr alpha(1)41 relative to the oxy hemoglobin as in human hemoglobin. And the tertiary structure changes of heme pocket and FG corner are also smaller than that in human hemoglobin. A unique mutation among avian and mammalian Hbs of alpha119 from proline to alanine at the alpha(1)beta(1 )interface in bar-headed goose hemoglobin brings a gap between Ala alpha119 and Leu beta55, the minimum distance between the two residues is 4.66 A. At the entrance to the central cavity around the molecular dyad, some residues of two beta chains form a positively charged groove where the inositol pentaphosphate binds to the hemoglobin. The His beta146 is at the inositol pentaphosphate binding site and the salt-bridge between His beta146 and Asp beta94 does not exist in the deoxy hemoglobin, which brings the weak chloride-independent Bohr effect to bar-headed goose hemoglobin.

Amino-acid sequence of the alpha D- and beta-polypeptide chains of the Japanese quail hemoglobin

Two hemoglobin components are recognized in the erythrocytes of the adult Japanese quail: a major (Q-II) and a minor (Q-I) component. We have determined the amino-acid sequence of the alpha D-globin of the minor component and the beta-globin which is common to both components by conventional protein sequence analysis. The sequences of both the alpha D- and the beta-globins showed close homology with those of their counterpart constituents in other avian hemoglobins. Proline at position 119 in the alpha D-globin which is known to be critical for the altitude respiration by the alpha 1 beta 1 interface is conserved in the Japanese quail hemoglobin.

Primary structure of hemoglobin alpha-chain from cuckoo (Eudynamys scolopaceae, cuculiformes)

The complete amino acid sequence of the alpha A-chain of major hemoglobin component from Cuckoo (Eudynamys scolopaceae) is presented. Separation of the polypeptide subunits was achieved by ion exchange chromatography in the presence of 8 M urea. The sequence was studied by automatic Edman degradation of the native chain and its tryptic fragments in a gas-phase sequencer. Comparison with other avian hemoglobins shows residues alpha 21, alpha 30, alpha 96, alpha 110, and alpha 114 as being specific to Cuckoo. The functional significance of these is discussed.

Primary structure of hemoglobin beta-chain from Columba livia (gray wild pigeon)

Primary structure of beta-chain of pigeon is presented. It was determined by amino acid sequence analysis of intact beta-chain and its peptides obtained by the enzymatic and chemical cleavage. Comparison of amino acid sequence of the chain with other available data shows beta 14 Ile, beta 61 Lys, and beta 113 Ile as residues specific to pigeon. One important replacement at alpha 1 beta 1 contact is beta 55 Met----Ser.

Cooperativity and allosteric regulation in non-mammalian vertebrate haemoglobins

1. This review illustrates the vast range of molecular functions expressed in non-mammalian vertebrate haemoglobins; with particular reference to the degree of aggregation of haemoglobin subunits and their interactions with allosteric effectors. 2. In at least the broadest sense, these properties suggest that haemoglobin function in non-mammalian vertebrates can be viewed against the evolutionary hierarchy of organisms rather than from a purely adaptive perspective.

Primary structure of hemoglobin from gray partridge (Francolinus pondacerianus, Galliformes)

The complete amino acid sequence of the alpha A-chain of major hemoglobin component from gray partridge Francolinus pondacerianus is presented. The major component HbA accounts for 75% of the total hemolysate. Separation of the globin subunits was achieved by ion-exchange chromatography on CM-Cellulose in 8 M urea. The sequence was studied by automatic Edman degradation of the native chain and its tryptic peptides in a gas-phase sequencer. The phylogenetic relationship of Galliformes with other avian orders is discussed.

Primary structure of hemoglobin alpha-chain of Columba livia (gray wild pigeon)

Primary structure of hemoglobin of alpha-chain of Columba livia is presented. The separation of alpha-chain was obtained from globin by ion-exchange chromatography (CMC-52) and reversed-phase HPLC (RP-2 column). Amino acid sequence of intact as well as tryptic digested chain was determined on gas-phase sequencer. Structure is aligned homologously with 21 other species. Among different exchanges, positions alpha 24 (Tyr----Leu), alpha 26 (Ala----Gly), alpha 32 (Met----Leu), alpha 64 (Asp----Glu), alpha 113 (Leu----Phe), and alpha 129 (Leu----Val) are unique to pigeon hemoglobin. The various exchanges in alpha-chain are discussed with reference to evolution and phylogeny. The results show that the order Columbiformes is evolutionarily closer to the order Anseriformes. Since the pigeon is homogeneous, having HbA (alpha A-chain) and lacks alpha D-chain, its phylogenetic placement could be established among birds having single hemoglobin components.

Primary structure of the hemoglobin alpha-chain of rose-ringed parakeet (Psittacula krameri)

The structure of the hemoglobin alpha-chain of Rose-ringed Parakeet was determined by sequence degradations of the intact subunit, the CNBr fragments, and peptides obtained by digestion with staphylococcal Glu-specific protease and trypsin. Using this analysis, the complete alpha-chain structure of 21 avian species is known, permitting comparisons of the protein structure and of avian relationships. The structure exhibits differences from previously established avian alpha-chains at a total of 61 positions, five of which have residues unique to those of the parakeet (Ser-12, Gly-65, Ser-67, Ala-121, and Leu-134). The analysis defines hemoglobin variation within an additional avian order (Psittaciformes), demonstrates distant patterns for evaluation of relationships within other avian orders, and lends support to taxonomic conclusions from molecular data.

[Molecular aspects of high altitude respiration of birds. Hemoglobins of the striped goose (Anser indicus), the Andean goose, (Chloephaga melanoptera) and vulture (Gyps rueppellii)]

Respiration of birds at high altitude and the structural adaptation of avian hemoglobins are studied. Applying the method of the "minimal biological distance", hemoglobins of closely related species were sequenced and compared with each other. Physiological measurements and sequence data show that adaptation to hypoxic stress can be interpreted as exchange of one amino acid. The structural aspects of the genetical data are discussed on the basis of the atomic model of hemoglobin. High-altitude respiration is not a general characteristic of birds: the adaptation to high altitudes is the result of a specific mutation, thus distinguishing a species from its closest relatives in the lowland.

High-altitude respiration of birds. The primary structures of the alpha D-chains of the Bar-headed Goose (Anser indicus), the Greylag Goose(Anser anser) and the Canada Goose (Branta canadensis)

The primary structures of the alpha D-chains of the minor component Hb D of Anser indicus, Anser anser and Branta canadensis are presented. Following chain separation by RP-HPLC, the amino-acid sequences were established by automatic Edman degradation of the globin chains and the tryptic peptides. The three chains show a high degree of homology. For the high altitude respiration the alpha 1 beta 1 interface at position alpha 119 is important. For the Bar-headed Goose a mechanism for high altitude respiration involving both Hb A having alanine at position 119 and Hb D having proline at that position is suggested. Furthermore, a possible genetical development of the avian alpha D-gene expression based on a new B alpha-box mutation in the three geese and an unusual 5' splice junction (GT/GC-transition) in the duck gene is discussed. We consider the possibility that the alpha D-gene is an intermediate between a functional gene, reduced in its expression, and a pseudogene.

Interaction of allosteric effectors with alpha-globin chains and high altitude respiration of mammals. The primary structure of two tylopoda hemoglobins with high oxygen affinity: vicuna (Lama vicugna) and alpaca (Lama pacos)

Polyacrylamide gel electrophoresis and ion-exchange chromatography revealed one hemoglobin component for vicuna (Lama vicugna) and alpaca (Lama pacos). Following chain separation by chromatography on carboxymethyl-cellulose, the amino-acid sequences were elucidated for the alpha- and beta-chains of both hemoglobins using automatic Edman degradation of the chains and the tryptic peptides. Vicuna and alpaca have identical beta-chains showing no substitutions to llama (Lama glama) either. In the alpha-chains alpaca differs from llama by the exchange of one amino-acid residue: alpha 122(H5)Asp----His. The same substitution is present in vicuna too, but in addition we found two more exchanges: alpha 10(A8)Ile----Val and alpha 130(H13)Ala----Thr. The close relationship between llama and alpaca suggests that they both originate from the wild guanaco, and there is no domesticated form of vicuna. The sequence data show that the higher oxygen affinity in vicuna compared to llama and alpaca must be due to the alpha-chains as the beta-chains are identical. The significance of the substitutions in alpha 122(H5), an alpha 1/beta 1-contact, and alpha 130(H13) is discussed.

[Primary structure of alpha and beta chains from the major hemoglobin component of the magpie goose (Anseranas semipalmata, Anatidae)]

The amino acid sequence of the alpha and beta chains from the major hemoglobin component (HbA) of Australian Magpie Goose (Anseranas semipalmata) is given. The minor component with the alpha D chains was detected, but only found in low concentrations. By homologous comparison, Greylag Goose hemoglobin (Anser anser) and Australian Magpie Goose alpha chains differ by 13 amino acids or 17 nucleotide (4 two point mutations) exchanges, beta chains by 6 exchanges. Seven alpha 1 beta 1 contacts are modified by substitutions in positions alpha 30-(B11)Glu leads to Gln, alpha 34(B15)Thr leads to Gln, alpha 35(B16)-Ala leads to Thr, alpha 36(B17)Tyr leads to Phe, beta 55(D6)Leu leads to Ile, beta 119(GH2)Ala leads to Ser and beta 125(H3)Glu leads to Asp. Further, one alpha 1 beta 2 contact point was changed in beta 39(C5)Gln leads to Glu. Mutation in this position, except in two abnormal human hemoglobins, was not found in any species. Amino acid exchanges between hemoglobin of Australian Magpie Goose and other birds are discussed.

The amino acid sequence of Canada goose (Branta canadensis) and mute swan (Cygnus olor) hemoglobins. Two different species with identical beta-chains

The amino acid sequences of the alpha- and beta-chains from the major hemoglobin component (HbA) of Canada goose (Branta canadensis) and mute swan (Cygnus olor) are given. The alpha-chains are of the alpha A-type, since alpha D-type was expressed but only found in low concentrations. By homologous comparison, greylag goose hemoglobin (Anser anser) and Canada goose hemoglobin alpha-chains differ by two exchanges, and beta-chains by three exchanges. A valine substitution for threonine was found at position alpha 34 (B15). This exchange is a result of a two point mutation. Thus, there are three nucleotide mutations in alpha-chains, as in beta-chains. Substitutions in positions alpha 34 (B15) and beta 125 (H3) have modified intersubunit contacts (alpha 1 beta 1-contacts). A comparison of mute swan hemoglobin with greylag goose hemoglobin shows four exchanges in alpha-chains and three in beta-chains. Canada goose and mute swan have identical beta-chains, while alpha-chains differ in two amino acids. One of these exchanges is implicated in one of the alpha 1 beta 1-contact points (alpha 34) where isoleucine substitution for valine was found. Comparison of hemoglobins from different species in the same tribe (Anserini) shows a high homology between Canada goose and mute swan hemoglobins.