Identification and characterization of tyrosine kinases in anole lizard indicate the conserved tyrosine kinase repertoire in vertebrates

Liu, Ake; He, Funan; Gu, Xun

doi:10.1007/s00438-017-1356-7

Cited by 9 publications

(12 citation statements)

References 60 publications

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“…Simionato et al [25] reported that gene family size does not generally reflect the evolutionary diversity of gene families, such as the tyrosine kinase family and the basic helix-loop-helix family [25][26][27]. Therefore, we tried to explore the difference in the OR gene numbers between marine and terrestrial mammals resulting from gene-specific duplications or increased numbers of gene gains and losses.…”

Section: Or Gene Numbers Of Marine Mammals Are Significantly Lower Thmentioning

confidence: 99%

Convergent degeneration of olfactory receptor gene repertoires in marine mammals

Liu

Shen

et al. 2019

Preprint

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Background: Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified, and the factors that might underlie these variations are unknown. Results: To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had fewer OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous genes in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions: Marine mammals have experienced large numbers of OR gene losses compared with their related terrestrial lineages, which may result from the frequent birth-and-death evolution under varied functional constrains. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.

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Section: Or Gene Numbers Of Marine Mammals Are Significantly Lower Thmentioning

confidence: 99%

Convergent degeneration of olfactory receptor gene repertoires in marine mammals

Liu

Shen

et al. 2019

Preprint

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“…Generally, TKs are categorized into 30 subfamilies [ 10 , 11 , 33 ]. The multiformity of TKs is likely to imply the complicacy of the pTyr-based signaling system [ 38 ].…”

Section: Resultsmentioning

confidence: 99%

“…In addition to the highly conserved TK domains, TK proteins also contain various functional protein domains interacting with other components within signal transduction pathways [ 9 ]. Based on kinase domain sequence and protein secondary structure, TKs are generally grouped into 30 subfamilies [ 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

“…Physiological effects and in vivo regulatory mechanisms of TKs have been interesting topics of research in recent years [ 29 , 30 ]. After years of research, TKs have been characterized in masses of species, and genome-wide systematic identification and characterization of this protein superfamily has also been conducted in many metazoans, including humans, amphioxus, zebra-fish and green anole lizard [ 10 , 11 , 31 , 32 , 33 ], providing numerous important insights into the structure, function, and regulation of TKs. Some important progress has also been made in the study of silkworm TKs recently [ 34 , 35 ].…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification and Characterization of Tyrosine Kinases in the Silkworm, Bombyx mori

Tong

Han

et al. 2018

IJMS

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The tyrosine kinases (TKs) are important parts of metazoan signaling pathways and play significant roles in cell growth, development, apoptosis and disease. Genome-wide characterization of TKs has been conducted in many metazoans, however, systematic information about this family in Lepidoptera is still lacking. We retrieved 33 TK-encoding genes in silkworm and classified them into 25 subfamilies by sequence analysis, without members in AXL, FRK, PDGFR, STYK1 and TIE subfamilies. Although domain sequences in each subfamily are conserved, TKs in vertebrates tend to be remarkably conserved and stable. Our results of phylogenetic analysis supported the previous conclusion for the second major expansion of TK family. Gene-Ontology (GO) analysis revealed that a higher proportion of BmTKs played roles in binding, catalysis, signal transduction, metabolism, biological regulation and response to stimulus, compared to all silkworm genes annotated in GO. Moreover, the expression profile analysis of BmTKs among multiple tissues and developmental stages demonstrated that many genes exhibited stage-specific and/or sex-related expression during embryogenesis, molting and metamorphosis, and that 8 BmTKs presented tissue-specific high expression. Our study provides systematic description of silkworm tyrosine kinases, and may also provide further insights into metazoan TKs and assist future studies addressing their functions.

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“…KCNMA1 is a pore forming α-subunit of the large-conductance calcium- and voltage-activated potassium channel linked to heightened proliferation and brain metastases [ 37 ]. NOK is a potent oncogene expressed in multiple cancers [ 38 ], which activates signaling pathways including MAPK and PI3K by phosphorylating them [ 39 ]. Clearly, all these genes are important and subject to complex regulation, among which are the “repressor” effects of SUMOylated PR-A.…”

Section: Discussionmentioning

confidence: 99%

SUMOylation Regulates Transcription by the Progesterone Receptor A Isoform in a Target Gene Selective Manner

et al. 2018

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Luminal breast cancers express estrogen (ER) and progesterone (PR) receptors, and respond to endocrine therapies. However, some ER+PR+ tumors display intrinsic or acquired resistance, possibly related to PR. Two PR isoforms, PR-A and PR-B, regulate distinct gene subsets that may differentially influence tumor fate. A high PR-A:PR-B ratio is associated with poor prognosis and tamoxifen resistance. We speculate that excessive PR-A marks tumors that will relapse early. Here we address mechanisms by which PR-A regulate transcription, focusing on SUMOylation. We use receptor mutants and synthetic promoter/reporters to show that SUMOylation deficiency or the deSUMOylase SENP1 enhance transcription by PR-A, independent of the receptors’ dimerization interface or DNA binding domain. De-SUMOylation exposes the agonist properties of the antiprogestin RU486. Thus, on synthetic promoters, SUMOylation functions as an independent brake on transcription by PR-A. What about PR-A SUMOylation of endogenous human breast cancer genes? To study these, we used gene expression profiling. Surprisingly, PR-A SUMOylation influences progestin target genes differentially, with some upregulated, others down-regulated, and others unaffected. Hormone-independent gene regulation is also PR-A SUMOylation dependent. Several SUMOylated genes were analyzed in clinical breast cancer database. In sum, we show that SUMOylation does not simply repress PR-A. Rather it regulates PR-A activity in a target selective manner including genes associated with poor prognosis, shortened survival, and metastasis.

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Identification and characterization of tyrosine kinases in anole lizard indicate the conserved tyrosine kinase repertoire in vertebrates

Cited by 9 publications

References 60 publications

Convergent degeneration of olfactory receptor gene repertoires in marine mammals

Convergent degeneration of olfactory receptor gene repertoires in marine mammals

Genome-Wide Identification and Characterization of Tyrosine Kinases in the Silkworm, Bombyx mori

SUMOylation Regulates Transcription by the Progesterone Receptor A Isoform in a Target Gene Selective Manner

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