Allosteric Hemoglobin Assembly: Diversity and Similarity

Royer, William E.; Zhu, Hao; Gorr, Thomas A.; Flores, Jason F.; Knapp, James E.

doi:10.1074/jbc.r500006200

Cited by 69 publications

(61 citation statements)

References 44 publications

(34 reference statements)

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“…Heat shock proteins are molecular chaperones that are evolutionarily conserved and important for regular cellular functions involving protein folding and unfolding, degradation and transport as well as stress responses (Sørensen et al, 2003). In contrast, globin genes are characterized by a high level of polymorphism, although on a protein level they maintain globin-fold and a conserved Histidine residue (Royer et al, 2005). From our de novo assemblies, we recovered polymorphic hemoglobin-like genes with preserved globin domains (Supplementary Table S3).…”

Section: Discussionmentioning

confidence: 99%

Unfolding the secrets of coral–algal symbiosis

et al. 2014

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Dinoflagellates from the genus Symbiodinium form a mutualistic symbiotic relationship with reefbuilding corals. Here we applied massively parallel Illumina sequencing to assess genetic similarity and diversity among four phylogenetically diverse dinoflagellate clades (A, B, C and D) that are commonly associated with corals. We obtained more than 30 000 predicted genes for each Symbiodinium clade, with a majority of the aligned transcripts corresponding to sequence data sets of symbiotic dinoflagellates and o2% of sequences having bacterial or other foreign origin. We report 1053 genes, orthologous among four Symbiodinium clades, that share a high level of sequence identity to known proteins from the SwissProt (SP) database. Approximately 80% of the transcripts aligning to the 1053 SP genes were unique to Symbiodinium species and did not align to other dinoflagellates and unrelated eukaryotic transcriptomes/genomes. Six pathways were common to all four Symbiodinium clades including the phosphatidylinositol signaling system and inositol phosphate metabolism pathways. The list of Symbiodinium transcripts common to all four clades included conserved genes such as heat shock proteins (Hsp70 and Hsp90), calmodulin, actin and tubulin, several ribosomal, photosynthetic and cytochrome genes and chloroplast-based hemecontaining cytochrome P450, involved in the biosynthesis of xanthophylls. Antioxidant genes, which are important in stress responses, were also preserved, as were a number of calcium-dependent and calcium/calmodulin-dependent protein kinases that may play a role in the establishment of symbiosis. Our findings disclose new knowledge about the genetic uniqueness of symbiotic dinoflagellates and provide a list of homologous genes important for the foundation of coral-algal symbiosis.

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Section: Discussionmentioning

confidence: 99%

Unfolding the secrets of coral–algal symbiosis

et al. 2014

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“…While allosteric mechanisms can be conserved within close taxonomic groups (6), anecdotal reports indicating that allostery is not a strong evolutionary driving force are increasingly commonplace (7)(8)(9). Surprisingly, diversity of response is even evident in hemoglobin (10,11), an archetype of long-range intramolecular communication. Clearly, conservation of allostery and intramolecular couplings is nowhere near that of structure and/or catalytic function (12).…”

Section: Introductionmentioning

confidence: 95%

A Critical Evaluation of Correlated Mutation Algorithms and Coevolution Within Allosteric Mechanisms

Livesay

Kreth

Fodor

2011

Methods in Molecular Biology

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The notion of using the evolutionary history encoded within multiple sequence alignments to predict allosteric mechanisms is appealing. In this approach, correlated mutations are expected to reflect coordinated changes that maintain intramolecular coupling between residue pairs. Despite much early fanfare, the general suitability of correlated mutations to predict allosteric couplings has not yet been established. Lack of progress along these lines has been hindered by several algorithmic limitations including phylogenetic artifacts within alignments masking true covariance and the computational intractability of consideration of more than two correlated residues at a time. Recent progress in algorithm development, however, has been substantial with a new generation of correlated mutation algorithms that have made fundamental progress toward solving these difficult problems. Despite these encouraging results, there remains little evidence to suggest that the evolutionary constraints acting on allosteric couplings are sufficient to be recovered from multiple sequence alignments. In this review, we argue that due to the exquisite sensitivity of protein dynamics, and hence that of allosteric mechanisms, the latter vary widely within protein families. If it turns out to be generally true that even very similar homologs display a wide divergence of allosteric mechanisms, then even a perfect correlated mutation algorithm could not be reliably used as a general mechanism for discovery of allosteric pathways.

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“…Giant extracellular hemoglobins, also known as erythrocruorins, have been investigated as a model of extreme complexity in oxygen-binding heme proteins [1][2][3]. They are characterized by a very high molecular mass (M) and their oligomeric structure together with the crowded and protected heme environment are two of the main factors responsible for the high redox stability.…”

Section: Introductionmentioning

confidence: 99%