The Evolution of Unusually Small Amelogenin Genes in Cetaceans; Pseudogenization, X–Y Gene Conversion, and Feeding Strategy

Kawasaki, Kazuhiko; Mikami, Masato; Goto, Mutsuo; Shindo, Junji; Amano, Masao; Ishiyama, Mikio

doi:10.1007/s00239-019-09917-0

Cited by 10 publications

(11 citation statements)

References 88 publications

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“…[19] Sequence alignment has been used to measure the conservation of HO-SLiMs and thereby gain a better understanding of their likely biological importance. The alignment was made using conserved exon/intron boundaries [23] and a unit residue scoring matrix. [11,19] Even so, the alignment of the longer P,Q-rich sequences in orthologues of the CSN2 (β-) and CSN3 (κ-) casein genes is uncertain in places, especially across the eutherian, metatherian, and monotreme lineages.…”

Section: Ho-slims In Caseinsmentioning

confidence: 99%

“…[11,19] Even so, the alignment of the longer P,Q-rich sequences in orthologues of the CSN2 (β-) and CSN3 (κ-) casein genes is uncertain in places, especially across the eutherian, metatherian, and monotreme lineages. [12,23] As with the amelogenins, the casein signal sequences are highly κ-casein, [76] may explain why residue mobility is lower in this region than in other casein sequences. [24][25][26] Although the discussion so far has emphasized the contribution of HO-SLiMs to intermolecular interactions, in the monomeric state intramolecular interactions may be favored.…”

Section: Ho-slims In Caseinsmentioning

confidence: 99%

“…Caseins are members of the paralogous group of secreted calcium (phosphate)-binding phosphoproteins (SCPPs) which play a major role in the control of biomineralization. [21][22][23] There are six known orthologous groups of casein genes, four members of which are expressed as the α S1 -, α S2 -, β-, and κ-casein constituents of bovine casein micelles, the large, heterogeneous particles that provide~80% of the protein component of this milk. In casein oligomers, many of the residues, including hydrophobic ones, are mobile.…”

mentioning

confidence: 99%

“…[35] Like caseins, they belong to the subgroup of paralogous SCPPs having a P,Q-rich sequence. [22,23,33,36] Three functional motifs can be identified in amelogenin (Supporting Information A Figure S1): (a) an N-terminal hydrophobic signal sequence, (b) a P,Q,Hrich central sequence which, unlike the casein P,Q-rich sequences, is fairly well conserved, [37] and (c) a short, highly charged, C-terminal sequence which, if deleted, produces uncontrolled aggregation. [17] The P,Q,H-rich mouse sequence has been further divided into an interaction region (Region A) near the N-terminus of the mature protein which is important in the entropic self-association of amelogenin to form dodecamers [38] and a sequence near its C-terminus (Region B) which is also implicated in the formation of nanospheres.…”

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confidence: 99%

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Sequence characteristics responsible for protein‐protein interactions in the intrinsically disordered regions of caseins, amelogenins, and small heat‐shock proteins

2019

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Milk caseins and dental amelogenins are intrinsically disordered proteins (IDPs) that associate with themselves and others. Paradoxically, they are also described as hydrophobic proteins, which is difficult to reconcile with a solvent‐exposed conformation. We attempt to resolve this paradox. We show that caseins and amelogenins are not hydrophobic proteins but they are more hydrophobic than most IDPs. Remarkably, uncharged residues from different regions of these mature proteins have a nearly constant average hydropathy but these regions exhibit different charged residue frequencies. A novel sequence analysis method was developed to identify hydrophobic and order‐promoting regions that would favor conformational collapse. We found that such regions were uncommon; most hydrophobic and order‐promoting residues were adjacent to hydrophilic or disorder‐promoting residues. A further reason why caseins and amelogenins do not collapse is their high proportion of disorder‐promoting proline residues. We conclude that in these proteins the hydrophobic effect is not large enough to cause conformational collapse but it can contribute, along with polar interactions, to protein‐protein interactions. This behaviour is similar to the interaction of the disordered N‐terminal region of small heat‐shock proteins with either themselves during oligomer formation or other, unfolding, proteins during chaperone action.

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Section: Ho-slims In Caseinsmentioning

confidence: 99%

Section: Ho-slims In Caseinsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Sequence characteristics responsible for protein‐protein interactions in the intrinsically disordered regions of caseins, amelogenins, and small heat‐shock proteins

2019

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“…Studies [28] indicate polymorphism of four Y chromosome genes of domestic pigs: USP9Y, UTY, AMELY, and EIF2s3Y. Based on available data [29][30][31][32], none of them seems to be an obvious candidate who could determine revealed interlinear differences (Table 1, 2). To evaluate the effectiveness of artificial selection by the large size of piglets in the genealogical lines of boars, a comparison was made of sample means with a desirable selection trait value of 700 g [17].…”

Section: *This Refers To the Relevance Of Differences Between The Carmentioning

confidence: 99%

Y chromosome effect on prenatal live weight growth of laboratory minipigs

et al. 2020

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This paper describes the results of the influence of Y-chromosome gene complex on pre- and postnatal growth of piglets of laboratory mini-pigs ICG SB RAS. Breeding group includes four genealogical lines of boars united by a successive father-son relationship. Three lines: MS2853, MS2987, and VTN300 inherited their Y chromosomes from boars of Vietnamese-South Asian breed. The fourth line (LNDR07) received Y chromosome from the Landrace boar. This study revealed that all three lines of boars carrying Asian Y chromosome did not differ in weight of newborn offspring, while the weight and, correspondingly, prenatal growth of newborns of boars carrying European Y chromosome were statistically significantly less. Thus, at this stage of research, there is reason to believe that the selection group of mini-pigs ICG SB RAS contains polymorphism in the complex of Y-chromosome genes involved in the control of prenatal growth process. An assumption was considered that growth retardation during prenatal and early postnatal periods, as well as an increased proportion of culled offspring of boars carrying European Y chromosome can be caused by poor compatibility of its gene complex with the allele pool inherited from the mini pigs ICG SB RAS from Vietnamese breed.

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Anatomical, Ontogenetic, and Genomic Homologies Guide Reconstructions of the Teeth-to-Baleen Transition in Mysticete Whales

et al. 2022

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The transition in Mysticeti (Cetacea) from capture of individual prey using teeth to bulk filtering batches of small prey using baleen ranks among the most dramatic evolutionary transformations in mammalian history. We review phylogenetic work on the homology of mysticete feeding structures from anatomical, ontogenetic, and genomic perspectives. Six characters with key functional significance for filter-feeding behavior are mapped to cladograms based on 11 morphological datasets to reconstruct evolutionary change across the teeth-to-baleen transition. This comparative summary within a common parsimony framework reveals extensive conflicts among independent systematic efforts but also broad support for the newly named clade Kinetomenta (Aetiocetidae + Chaeomysticeti). Complementary anatomical studies using CTscans and ontogenetic series hint at commonalities between the developmental programs for teeth and baleen, lending further support for a 'transitional chimaeric feeder' scenario that best explains current knowledge on the transition to filter feeding. For some extant mysticetes, the ontogenetic sequence in fetal specimens recapitulates the inferred evolutionary transformation: from teeth, to teeth and baleen, to just baleen. Phylogenetic mapping of inactivating mutations reveals mutational decay of 'dental genes' related to enamel formation before the emergence of crown Mysticeti, while 'baleen genes' that were repurposed or newly derived during the evolutionary elaboration of baleen currently are poorly characterized. Review and meta-analysis of available data suggest that the teeth-to-baleen transition in Mysticeti ranks among the best characterized macroevolutionary shifts due to the diversity of data from the genome, the fossil record, comparative anatomy, and ontogeny that directly bears on this remarkable evolutionary transformation.

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The Evolution of Unusually Small Amelogenin Genes in Cetaceans; Pseudogenization, X–Y Gene Conversion, and Feeding Strategy

Cited by 10 publications

References 88 publications

Sequence characteristics responsible for protein‐protein interactions in the intrinsically disordered regions of caseins, amelogenins, and small heat‐shock proteins

Sequence characteristics responsible for protein‐protein interactions in the intrinsically disordered regions of caseins, amelogenins, and small heat‐shock proteins

Y chromosome effect on prenatal live weight growth of laboratory minipigs

Anatomical, Ontogenetic, and Genomic Homologies Guide Reconstructions of the Teeth-to-Baleen Transition in Mysticete Whales

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