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Tribbles in the 21st Century: The Evolving Roles of Tribbles Pseudokinases in Biology and Disease

View Article: PubMed Central - PubMed

ABSTRACT

The Tribbles (TRIB) pseudokinases control multiple aspects of eukaryotic cell biology and evolved unique features distinguishing them from all other protein kinases. The atypical pseudokinase domain retains a regulated binding platform for substrates, which are ubiquitinated by context-specific E3 ligases. This plastic configuration has also been exploited as a scaffold to support the modulation of canonical MAPK and AKT modules. In this review, we discuss the evolution of TRIBs and their roles in vertebrate cell biology. TRIB2 is the most ancestral member of the family, whereas the emergence of TRIB3 homologs in mammals supports additional biological roles, many of which are currently being dissected. Given their pleiotropic role in diseases, the unusual TRIB pseudokinase conformation provides a highly attractive opportunity for drug design.

No MeSH data available.


Distinguishing Sequence and Structural Features of Tribbles (TRIB) Pseudokinases. (A) Constraints that help distinguish TRIB kinases from all other kinases are shown in a contrast hierarchical alignment, where representative TRIB kinases from diverse organisms constitute the display alignment; all TRIB-like sequences available (492 sequences, September 2016) constitute the foreground alignment, and related CAMK sequences (79 487 sequences) constitute the background alignment. Complete foreground and background alignments are not shown due to the hundreds of text pages required. Instead, information encoded in these large alignments is shown as residue frequencies directly below the display alignment where, for example, the number ‘5′ indicates that the corresponding residue occurs 50–60% of the time at the corresponding position. The histogram above the alignment plots the strength of the selective pressure shifting residues at each position in the TRIB kinases away from the residue composition observed at the corresponding positions in CAMKs. Residue positions subject to the strongest constraints are highlighted with chemically similar amino acids colored similarly; weakly conserved positions and nonconserved positions are shown in dark and light gray, respectively. Dots below the histograms indicate those residue positions that most strikingly distinguish TRIB kinases from CAMKs as selected by the Bayesian pattern partitioning procedure [94]. Key secondary structural elements are indicated above the alignment; amino acid numbering corresponds to human TRIB2. Identifiers for TRIB sequences used in the display alignment can be compared with canonical kinase sequences by inspecting Box 1. (B,C) Modeling of the structural disposition of TRIB-specific residues forming the regulatory activation loop, atypical DFG motif (E[S/N]LED), and αC helix in human TRIB2. The kinked αC-helix is shown in yellow and the activation loop (A-loop) is shown in magenta. TRIB family conserved residues are shown in green. Putative hydrogen-bonding interactions in the modeled structure are shown by broken lines and the putative substrate-binding site in the C-lobe is labeled. Structural image was generated using PyMoL. Specific TRIB gene identifiers are listed in the legend to Figure 4.
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fig0015: Distinguishing Sequence and Structural Features of Tribbles (TRIB) Pseudokinases. (A) Constraints that help distinguish TRIB kinases from all other kinases are shown in a contrast hierarchical alignment, where representative TRIB kinases from diverse organisms constitute the display alignment; all TRIB-like sequences available (492 sequences, September 2016) constitute the foreground alignment, and related CAMK sequences (79 487 sequences) constitute the background alignment. Complete foreground and background alignments are not shown due to the hundreds of text pages required. Instead, information encoded in these large alignments is shown as residue frequencies directly below the display alignment where, for example, the number ‘5′ indicates that the corresponding residue occurs 50–60% of the time at the corresponding position. The histogram above the alignment plots the strength of the selective pressure shifting residues at each position in the TRIB kinases away from the residue composition observed at the corresponding positions in CAMKs. Residue positions subject to the strongest constraints are highlighted with chemically similar amino acids colored similarly; weakly conserved positions and nonconserved positions are shown in dark and light gray, respectively. Dots below the histograms indicate those residue positions that most strikingly distinguish TRIB kinases from CAMKs as selected by the Bayesian pattern partitioning procedure [94]. Key secondary structural elements are indicated above the alignment; amino acid numbering corresponds to human TRIB2. Identifiers for TRIB sequences used in the display alignment can be compared with canonical kinase sequences by inspecting Box 1. (B,C) Modeling of the structural disposition of TRIB-specific residues forming the regulatory activation loop, atypical DFG motif (E[S/N]LED), and αC helix in human TRIB2. The kinked αC-helix is shown in yellow and the activation loop (A-loop) is shown in magenta. TRIB family conserved residues are shown in green. Putative hydrogen-bonding interactions in the modeled structure are shown by broken lines and the putative substrate-binding site in the C-lobe is labeled. Structural image was generated using PyMoL. Specific TRIB gene identifiers are listed in the legend to Figure 4.

Mentions: TRIB pseudokinases are predicted to be three-domain proteins containing an N-terminal PEST region, a pseudokinase domain (containing an unusual N-lobe and a canonical C-lobe) and a C-terminal COP1-binding peptide region, which interacts in cis with a pocket formed adjacent to the unusual αC-helix found in the TRIB pseudokinase domain (Figure 1). Recent structural analysis of the human TRIB1 pseudokinase domain [14] confirms an atypical kinase fold that diverges most notably in the N-lobe, which harbors most of the catalytic machinery, but which preserves a putative substrate-binding site in the C-lobe of the kinase domain. No structural information has been reported for the N-terminal PEST domain, or for any domains of the TRIB2 or TRIB3 pseudokinases. Although these same defining regions are conserved across TRIB polypeptides when comparing the pseudokinase domain with catalytically active CAMK relatives (Box 1), the availability of tens of thousands of protein kinase-like sequences from diverse organisms provides a timely opportunity to define distinguishing or unique features of TRIB pseudokinases using statistical comparisons of large data sets. Such approaches across kinomes have previously been invaluable to provide new insights into protein kinase structure, function, and evolution 37, 38, 39, 40, 41, 42. As collated in Figure 3, a Bayesian statistical comparison reveals strong selective constraints imposed on each of the individual TRIB kinase sequences during evolution. At a gross level, these constraints correspond to ‘TRIB-specific’ residues and/or motifs that are highly conserved in TRIB kinases but strikingly different in the closely related pseudokinase SgK495 and the broader family of canonical CAMKs. We focus on the most distinctive features in the core (conserved) regions of the TRIB family, namely the pseudokinase domain (Figure 3A) and flanking C-terminal tail (Figure 4A). In passing, we note that the N-terminal PEST domain contains distinct sequence motifs that are characteristic of each TRIB variant, and these subfamily specific motifs are assumed to regulate distinct protein turnover patterns in both ‘normal’ and disease-associated cells 43, 44.


Tribbles in the 21st Century: The Evolving Roles of Tribbles Pseudokinases in Biology and Disease
Distinguishing Sequence and Structural Features of Tribbles (TRIB) Pseudokinases. (A) Constraints that help distinguish TRIB kinases from all other kinases are shown in a contrast hierarchical alignment, where representative TRIB kinases from diverse organisms constitute the display alignment; all TRIB-like sequences available (492 sequences, September 2016) constitute the foreground alignment, and related CAMK sequences (79 487 sequences) constitute the background alignment. Complete foreground and background alignments are not shown due to the hundreds of text pages required. Instead, information encoded in these large alignments is shown as residue frequencies directly below the display alignment where, for example, the number ‘5′ indicates that the corresponding residue occurs 50–60% of the time at the corresponding position. The histogram above the alignment plots the strength of the selective pressure shifting residues at each position in the TRIB kinases away from the residue composition observed at the corresponding positions in CAMKs. Residue positions subject to the strongest constraints are highlighted with chemically similar amino acids colored similarly; weakly conserved positions and nonconserved positions are shown in dark and light gray, respectively. Dots below the histograms indicate those residue positions that most strikingly distinguish TRIB kinases from CAMKs as selected by the Bayesian pattern partitioning procedure [94]. Key secondary structural elements are indicated above the alignment; amino acid numbering corresponds to human TRIB2. Identifiers for TRIB sequences used in the display alignment can be compared with canonical kinase sequences by inspecting Box 1. (B,C) Modeling of the structural disposition of TRIB-specific residues forming the regulatory activation loop, atypical DFG motif (E[S/N]LED), and αC helix in human TRIB2. The kinked αC-helix is shown in yellow and the activation loop (A-loop) is shown in magenta. TRIB family conserved residues are shown in green. Putative hydrogen-bonding interactions in the modeled structure are shown by broken lines and the putative substrate-binding site in the C-lobe is labeled. Structural image was generated using PyMoL. Specific TRIB gene identifiers are listed in the legend to Figure 4.
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fig0015: Distinguishing Sequence and Structural Features of Tribbles (TRIB) Pseudokinases. (A) Constraints that help distinguish TRIB kinases from all other kinases are shown in a contrast hierarchical alignment, where representative TRIB kinases from diverse organisms constitute the display alignment; all TRIB-like sequences available (492 sequences, September 2016) constitute the foreground alignment, and related CAMK sequences (79 487 sequences) constitute the background alignment. Complete foreground and background alignments are not shown due to the hundreds of text pages required. Instead, information encoded in these large alignments is shown as residue frequencies directly below the display alignment where, for example, the number ‘5′ indicates that the corresponding residue occurs 50–60% of the time at the corresponding position. The histogram above the alignment plots the strength of the selective pressure shifting residues at each position in the TRIB kinases away from the residue composition observed at the corresponding positions in CAMKs. Residue positions subject to the strongest constraints are highlighted with chemically similar amino acids colored similarly; weakly conserved positions and nonconserved positions are shown in dark and light gray, respectively. Dots below the histograms indicate those residue positions that most strikingly distinguish TRIB kinases from CAMKs as selected by the Bayesian pattern partitioning procedure [94]. Key secondary structural elements are indicated above the alignment; amino acid numbering corresponds to human TRIB2. Identifiers for TRIB sequences used in the display alignment can be compared with canonical kinase sequences by inspecting Box 1. (B,C) Modeling of the structural disposition of TRIB-specific residues forming the regulatory activation loop, atypical DFG motif (E[S/N]LED), and αC helix in human TRIB2. The kinked αC-helix is shown in yellow and the activation loop (A-loop) is shown in magenta. TRIB family conserved residues are shown in green. Putative hydrogen-bonding interactions in the modeled structure are shown by broken lines and the putative substrate-binding site in the C-lobe is labeled. Structural image was generated using PyMoL. Specific TRIB gene identifiers are listed in the legend to Figure 4.
Mentions: TRIB pseudokinases are predicted to be three-domain proteins containing an N-terminal PEST region, a pseudokinase domain (containing an unusual N-lobe and a canonical C-lobe) and a C-terminal COP1-binding peptide region, which interacts in cis with a pocket formed adjacent to the unusual αC-helix found in the TRIB pseudokinase domain (Figure 1). Recent structural analysis of the human TRIB1 pseudokinase domain [14] confirms an atypical kinase fold that diverges most notably in the N-lobe, which harbors most of the catalytic machinery, but which preserves a putative substrate-binding site in the C-lobe of the kinase domain. No structural information has been reported for the N-terminal PEST domain, or for any domains of the TRIB2 or TRIB3 pseudokinases. Although these same defining regions are conserved across TRIB polypeptides when comparing the pseudokinase domain with catalytically active CAMK relatives (Box 1), the availability of tens of thousands of protein kinase-like sequences from diverse organisms provides a timely opportunity to define distinguishing or unique features of TRIB pseudokinases using statistical comparisons of large data sets. Such approaches across kinomes have previously been invaluable to provide new insights into protein kinase structure, function, and evolution 37, 38, 39, 40, 41, 42. As collated in Figure 3, a Bayesian statistical comparison reveals strong selective constraints imposed on each of the individual TRIB kinase sequences during evolution. At a gross level, these constraints correspond to ‘TRIB-specific’ residues and/or motifs that are highly conserved in TRIB kinases but strikingly different in the closely related pseudokinase SgK495 and the broader family of canonical CAMKs. We focus on the most distinctive features in the core (conserved) regions of the TRIB family, namely the pseudokinase domain (Figure 3A) and flanking C-terminal tail (Figure 4A). In passing, we note that the N-terminal PEST domain contains distinct sequence motifs that are characteristic of each TRIB variant, and these subfamily specific motifs are assumed to regulate distinct protein turnover patterns in both ‘normal’ and disease-associated cells 43, 44.

View Article: PubMed Central - PubMed

ABSTRACT

The Tribbles (TRIB) pseudokinases control multiple aspects of eukaryotic cell biology and evolved unique features distinguishing them from all other protein kinases. The atypical pseudokinase domain retains a regulated binding platform for substrates, which are ubiquitinated by context-specific E3 ligases. This plastic configuration has also been exploited as a scaffold to support the modulation of canonical MAPK and AKT modules. In this review, we discuss the evolution of TRIBs and their roles in vertebrate cell biology. TRIB2 is the most ancestral member of the family, whereas the emergence of TRIB3 homologs in mammals supports additional biological roles, many of which are currently being dissected. Given their pleiotropic role in diseases, the unusual TRIB pseudokinase conformation provides a highly attractive opportunity for drug design.

No MeSH data available.