Studies on the structure of aldolase A from chicken muscle

Sequencing refractory regions in bird genomes are hotspots for accelerated protein evolution

Background

Approximately 1000 protein encoding genes common for vertebrates are still unannotated in avian genomes. Are these genes evolutionary lost or are they not yet found for technical reasons? Using genome landscapes as a tool to visualize large-scale regional effects of genome evolution, we reexamined this question.

Results

On basis of gene annotation in non-avian vertebrate genomes, we established a list of 15,135 common vertebrate genes. Of these, 1026 were not found in any of eight examined bird genomes. Visualizing regional genome effects by our sliding window approach showed that the majority of these "missing" genes can be clustered to 14 regions of the human reference genome. In these clusters, an additional 1517 genes (often gene fragments) were underrepresented in bird genomes. The clusters of “missing” genes coincided with regions of very high GC content, particularly in avian genomes, making them “hidden” because of incomplete sequencing. Moreover, proteins encoded by genes in these sequencing refractory regions showed signs of accelerated protein evolution. As a proof of principle for this idea we experimentally characterized the mRNA and protein products of four "hidden" bird genes that are crucial for energy homeostasis in skeletal muscle: ALDOA, ENO3, PYGM and SLC2A4.

Conclusions

A least part of the “missing” genes in bird genomes can be attributed to an artifact caused by the difficulty to sequence regions with extreme GC% (“hidden” genes). Biologically, these “hidden” genes are of interest as they encode proteins that evolve more rapidly than the genome wide average. Finally we show that four of these “hidden” genes encode key proteins for energy metabolism in flight muscle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01905-7.

Affinity labeling of rabbit muscle fructose-1,6-bisphosphate aldolase with 5'-[p-(fluorosulfonyl)benzoyl]-1,N6-ethenoadenosine

Aldolase contains one tight binding site and one weak binding site per subunit for ATP [Kasprzak, A. and Kochman, M. (1980) Eur. J. Biochem. 104, 443-450]. The reaction of the ATP analog 5'-[p-(fluorosulfonyl)benzoyl]-1,N6-ethenoadenosine with rabbit aldolase A results in linear inactivation of enzyme with respect to covalent linkage of fluorescent label. The enzyme is completely protected against modification in the presence of saturating covalent binding (k2 = 0.033 min-1) is preceded by a fast reversible binding step (Ki = 6.8 mM). Chemical modification of aldolase leads to formation of stable N epsilon (4-carboxybenzenesulfonyl-lysine (Cbs-Lys) and O-(4-carboxybenzenesulfonyl-tyrosine (Cbs-Tyr) derivatives. Almost all Cbs-Lys was found in the N-terminal CNBr peptide (CN-1), whereas Cbs-Tyr was present both in the N-terminal (CN-1) and C-terminal (CN-2) peptide. From carboxypeptidase digestion and tryptic peptide analysis, Cbs-Lys was localized in position 107, a small part of Cbs-Tyr was detected in position 84, and the majority of Cbs-Tyr was found in the C-terminal position Tyr-363. We conclude that the covalent binding of the ATP analog occurs at the mononucleotide tight-binding site of aldolase and is associated with modification of Lys-107 and Tyr-363. This conclusion is based on the measurements of enzymatic activity loss as a function of ATP analog incorporation as well as on previous data. It is postulated that Lys-107, which is the C-6 phosphate binding site for fructose-1,6-P2, is in close proximity to the functionally important Tyr-363. The rather small extent of modification of Tyr-84 (0.15 mol/subunit), is due either to nonspecific protein modification or labeling of the weak mononucleotide binding site.

o-Phthalaldehyde, a fluorescence probe of aldolase active site

Conditions were determined in which approximately one mole of omicron-phthalaldehyde reacts with one mole of aldolase subunit yielding a stable fluorescent isoindole derivative. During this chemical modification, a linear relationship was observed between the enzyme inactivation and absorbance change (337 nm) or fluorescence change (lambda em 420 nm, and lambda ex 338 nm) characteristic for isoindole ring formation. The reaction follows second-order kinetics, k = 1.1 X 10(3) M-1 S-1, in 50 mM borate buffer, pH 8.4 at 25 degrees C. The modification of aldolase results in loss of approximately one -SH group per protein subunit. The enzyme is protected against modification by substrates and competitive inhibitors. Essentially no isoindole derivative is formed when the glycerol-1-phosphate-lysyl derivative of aldolase is used for modification studies. It is concluded that aldolase modification occurs at the active-site region. Isolation of cross-linked peptides suggests that Lys-227 and Cys-336 are involved in formation of the isoindole derivative. This result supports Cys-336 as the active-site cysteine necessary for aldolase catalytic activity. Fluorescence studies have shown that the isoindole group linked to aldolase has its lambda max, em markedly shifted toward shorter wavelength in comparison to the fluorescence of free isoindole derivatives in aqueous solution. In model studies a linear relationship between lambda max, em of 1-(beta-hydroxyethylthio)-2-beta-hydroxyethylisoindole and the solvent polarity or acidity was observed. The results of the studies suggest that the microenvironment of the cleft in aldolase which binds isoindole appears to be of low acidity and low polarity. The apparent low polarity experienced by the isoindole probe may be due to its location in an actual low-polarity portion of the active site, or may be due to non-relaxing surroundings of the probe.