Ssu72 Results: Difference between revisions

From MDWiki
Jump to navigationJump to search
No edit summary
 
(24 intermediate revisions by 2 users not shown)
Line 61: Line 61:
==Evolution==
==Evolution==
===Multiple sequence alignment===
===Multiple sequence alignment===
The psiBLASTp searches showed that sequences homologous to Ssu72 are present in many genomes - many of the results were predicted genes in whole genome annotations. Also, the results indicate that some organisms have more than one copy of the gene- for example, Homo sapiens has a match on chromosome 21 (Gene ID 419410) and on chromosome 11 (Gene ID 390031). Other organisms with multiple copies are Pan Troglodytes (chromosomes 11: 745998 and X: 473738) and Canis familiaris (chromosomes 5: 479567 and 21: 485220).
The psiBLASTp searches show that sequences homologous to Ssu72 are present in many genomes - many of the results are predicted genes in whole genome annotations. Also, the results indicate that some organisms have more than one copy of the gene- for example, Homo sapiens has a match on chromosome 21 (Gene ID 419410) and on chromosome 11 (Gene ID 390031). Other organisms with multiple copies are Pan Troglodytes (chromosomes 11: 745998 and X: 473738) and Canis familiaris (chromosomes 5: 479567 and 21: 485220).


The SwissProt sequences align well, with occasional insertions/deletions. In particular, the Pezizomycotina share two large additional regions in comparison to the drosophila. Four of the yeasts also share a region. (The alignment with the Pezizomycotina region is a calculation error). Debaromyces hasenii also contains two additional regions.  
The SwissProt sequences align well, with occasional insertions/deletions (see figure 20). In particular, the Pezizomycotina share two large additional regions in comparison to Drosophila. Four of the yeasts also share a unique region. (The alignment with the Pezizomycotina region is spurious). Debaromyces hasenii also contains two additional regions.  


The regions that form the active site (the catalytic residues and the aspartate loop) are highly conserved. Other conserved regions fall within secondary structure features (helices, sheets, hairpin turns).  
The regions that form the active site (the catalytic residues and the aspartate loop) are highly conserved. Other conserved regions fall within secondary structure features (helices, sheets, hairpin turns).  


An alignment of sequences from all the NCBI databases shows a very similar pattern of conserved residues over 78 different organisms. In particular, the key residues in the active site are either invariant or very highly conserved.
An alignment of sequences from all the NCBI databases (figure 21) shows a very similar pattern of conserved residues over 78 different organisms. In particular, the key residues in the active site are either invariant or very highly conserved.


The alignment to the eight phosphatases shows that the catalytic residues are the same in the target protein (3fdf) and the phosphatases. However, the aspartate loop in the phosphatases is smaller and further along the sequence. Most of these are sequences of tyrosine (or related) phosphatases, with the exception of the acid phosphatase, 2p4u.
The alignment to the eight phosphatases (figure 22) shows that the catalytic residues are the same in the target protein (3fdf) and the phosphatases. However, the aspartate loop in the tyrosine phosphatases is smaller and further along the sequence. Most of these are sequences of tyrosine (or related) phosphatases, with the exception of the acid phosphatase, 2p4u.


<center><gallery widths="200px" heights="130px" perrow="4">
<center><gallery widths="300px" heights="200px" perrow="4">
image:AnnotatedMSA2str.jpg|'''Figure 20''': An alignment of the SwissProt sequences, and the target protein, annotated to show the active site regions and the secondary structures corresponding to the conserved regions.
image:AnnotatedMSA2str.jpg|'''Figure 20''': An alignment of the SwissProt sequences, and the target protein, annotated to show the active site regions and the secondary structures corresponding to the conserved regions.
image:SelNonredundantMSA.PNG|'''Figure 21''': An alignment of sequences from 78 organisms. The active site is conserved, as are many of the regions shown in the annotated SwissProt alignment.
image:SelNonredundantMSA.PNG|'''Figure 21''': An alignment of sequences from 78 organisms. The active site is conserved, as are many of the regions shown in the annotated SwissProt alignment.
Line 78: Line 78:


===Phylogenetic tree===
===Phylogenetic tree===
The tree corresponds perfectly to the current taxonomy. The overall grouping is into three branches: Fungi, Amoebozoa and Metazoa. Clear splits in the taxonomy, such as the one between Danio rerio (zebrafish) and the tetrapods, correspond to very high bootstrap values.  Low bootstrap occur when the organisms cannot be ranked based on this protein sequence alone. In some cases, this is because three groups may really be equidistant: for example, Shizosaccharomyces pombe belongs to neither the Pezizomycotina nor to the Saccharomycetales, and the bootstrap value of 56% indicates that a three-way split would be more appropriate. In other cases, such as the cluster of four yeasts (Candida glabrate, etc.) and the group of tetrapods (Xenopus laevis etc.), the organisms are too similar to be ranked with so little information, and the low bootstrap values reflect this.  
The tree corresponds perfectly to the current taxonomy (figures 23 and 24). The overall grouping is into three branches: Fungi, Amoebozoa and Metazoa. Clear splits in the taxonomy, such as the one between Danio rerio (zebrafish) and the tetrapods, correspond to very high bootstrap values.  Low bootstrap values occur when the organisms cannot be ranked based on this protein sequence alone. In some cases, this is because three groups may really be equidistant: for example, Shizosaccharomyces pombe belongs to neither the Pezizomycotina nor to the Saccharomycetales, and the bootstrap value of 56% indicates that a three-way split between the groups would be more appropriate. In other cases, such as the cluster of four yeasts (Candida glabrate, etc.) and the group of tetrapods (Xenopus laevis etc.), the organisms are too similar to be ranked given this highly conserved protein, and the low bootstrap values reflect this.  


The tree contains a variety of organisms. The tree does not have any unusual features that would need more organisms to clarify, but it would be useful to include more. In particular, plants are not represented at all. However it seems likely from these results that additional organisms that are included will also follow the known phylogeny.
The tree contains a variety of organisms. The tree does not have any unusual features that need clarification, but it would still be interesting to include more organisms. In particular, plants are not represented at all. However it seems likely from these results that even with additional sequences the tree will still follow known phylogeny.  


<center><gallery widths="600px" heights="400px" perrow="1">
<center><gallery widths="450px" heights="300px" perrow="2">
image:3fdfTree2.jpg|'''Figure 23''': Phylogenetic tree.
image:3fdfTree2.jpg|'''Figure 23''': Phylogenetic tree.
image:3fdfTree2inset.JPG|'''Figure 24''': A closer view of the Metazoa.
</gallery></center>
</gallery></center>


==Structure==
==Structure==
Structure determined using XRD. The following images were obtained using RasMol.
PDB 3fdf protein  - Secondary Structures
[[Image:3fdf.jpeg]]
PDB 3fdf protein  - Chains
[[Image:3fdf_2.jpeg]]
PDB 3fdf protein  - Molecular surface
[[Image:3fdfms.jpeg]]
----
    Protein Structure Database Searching by DaliLite v. 3
The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB).
These are the chains of different molecules that best matched to the Ssu72 RNA polymerase II CTD phosphatase homolog (it is important to notice that the first match corresponds to the protein that is being researched).
PDB ID ...    Z    rmsd lali nres  %id PDB  Description
3fdf-A.....    37.3  0.0  191  191  100 PDB  MOLECULE: '''FR253;''' 
3fmv-H...    32.4  0.6  190  190  100 PDB  MOLECULE: '''SERINE PHOSPHATASE OF RNA POLYMERASE II CTD;''' 
1dg9-A...    11.4  2.3  120  157  13 PDB  MOLECULE: '''TYROSINE PHOSPHATASE;'''
1rxi-A......    9.9  2.4  109  131  15 PDB  MOLECULE: '''ARSENATE REDUCTASE;'''
  DaliLite results: Multiple Structure Alignment
[[Image:Multipleestructuralalignmenta.jpeg]]
[[Image:Multiplestructuralalgnmentb.jpeg]]
  DalaLite results: Superimposed structures
FR253-TYROSINE PHOSPHATASE
[[Image:3fdf_1dg9.jpeg]]
FR253-ARSENATE REDUCTASE
[[Image:3fdf_1rxi.jpeg]]
FR253-SERINE PHOSPHATASE OF RNA POLYMERASE II CTD
[[Image:3fdf_3fmv.jpeg]]
----
Secondary Structures
FR253
[[Image:3fdfss.jpeg]]
SERINE PHOSPHATASE OF RNA POLYMERASE II CTD
[[Image:3fmvss.jpeg]]
TYROSINE PHOSPHATASE
[[Image:1dg9ss.jpeg]]
ARSENATE REDUCTASE
[[Image:1rxiss.jpeg]]
----
  3fdf vs 1dg9
Drosophila
[[Image:3fdf.jpg]]
Tyrosine Phosphatase
[[Image:1dg9.jpg]]
----
  STRING - Known and Predicted Protein-Protein Interactions
[[Image:Confidence.png]]
[[Image:Confidence.jpeg]]
----
  Homo sapiens homolog
Structure obtained through Swiss-Model Automatic Modelling Mode
[[Image:Humanhomolog.jpeg]]
Superimposition, using Dali server, between Homo sapiens homolog and 3fdf-A
[[Image:Human-3fdf.jpeg]]
Structure Alignment
[[Image:Super1.jpeg]]
[[Image:Super2.jpeg]]
===Heading===
===Heading===



Latest revision as of 02:25, 16 June 2009

Function

BLAST results

Running a protein BLAST search on 'serine phosphatase of RNA polymerase II CTD (SSU72 superfamily)' from Drosophila melenogaster (the 'Drosophila Ssu72 protein') returned a large number of highly 'relevant' (bit score > 200) sequences that were of a very similar length (see Figure 1) to that of the query. However, the first 27 of those sequences were not considered relevant for the purposes of this paper for a number of reasons. For instance, some were merely homologous proteins in other closely related Drosophila species that had been identified in a similarly automated manner to this one and for which there were no PubMed publications available and thus no information that could be used to easily infer functionally relevant details. Similarly, other proteins, in more distantly related organisms, had not been functionally characterised by experimentation or structural analysis, presumably because they had been identified by high-throughput sequencing and had seen minimal, if any, human input. Some BLAST hits were labelled as hypothetical proteins and were therefore not necessarily protein coding and biologically expressed. Notwithstanding this, the first relevant protein identified was 'SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae)', the human Ssu72 protein, for which there were a small number of articles available on PubMed (see Figure 2), as well as expression data from SymAtlas (see Figure 3). This protein was also found to have a 60.21% sequence identity with the Drosophila Ssu72 protein, with no gaps in the alignment. Thus, a review of the literature surrounding it was considered a suitable entry-point in the process of this analysis.


Literature review and ProFunc results

The human Ssu72 protein, for which there exist a number of eukaryotic homologues (Sun and Hampsey 1996), was first proposed to function as a protein tyrosine phosphatase (Meinhart, Silberzahn, & Cramer, 2003). Therefore, given this functional information about an analogous protein, a ProFunc analysis was carried out on our candidate protein, Drosophila Ssu72, with the purpose of comparing components of its primary and secondary structure with proteins that do not necessarily have a high level of overall sequence similarity – thus being unlikely to surface on a non-targeted search of a large database (ie. by BLAST) – but which may have shared catalytic domains. Despite offering a number of powerful results (see Figures 5 - 9), the ProFunc analysis of the Drosophila Ssu72 protein returned just two sets of informative data. The first of these was from the SSM (Secondary Structure Matching) program, which 'identifies proteins in the PDB that have a similar fold to that of the query structure' (Krissinel & Henrick, 2004). The summary of the results of this analysis (see Figures 10 and 11) is by itself promising, as the program exclusively returned proteins which function as phosphatases, all but one of which specifically has phospho-tyrosine as a substrate.

In the next set of results, generated by the so-called 'reverse template' program, the '[target] structure ... is broken up into a large number of templates and these in turn are scanned against a representative set of structures in the PDB' (Laskowski, Watson & Thornton, 2005). In effect, triads of residues from the queried protein are compared against a database of known catalytic sites for matches. The summary of the results (see Figures 12 and 13) show that, while there is only a low level of overall sequence identity (~ 20%) between the target structure and the hits returned by the program, the Drosophila Ssu72 protein shares three important residues - Val12(A), Cys13(A), Ser20(A) - with a number of different protein tyrosine phosphatases and that these residues occupy equivalent coordinates within their respective 3-D structures (see Figures 14 - 16). The implications of these results will follow in the 'function' section of the discussion.



Experimental evidence found in the literature, however, suggests that the human Ssu72 protein functions not as a tyrosine phosphatase, but as a serine phosphatase with specificity to the S5-P of the C-terminal domain of RNA Polymerase II (Krishnamurthy et al., 2004). Further, it also has a role in 3' mRNA processing (He et al., 2003), which is independent of its phosphatase activity (Krishnamurthy et al., 2004). However, there is nothing in the literature which suggests a mechanism by which this specificity to phospho-serine is conferred.

STRING results

Unfortunately, a search of the STRING database did not return any results for the Drosophila Ssu72 protein (see Figure 17). However, a number of interactions were returned when the amino acid sequence of the human protein was searched (see Figure 18). Somewhat disappointingly, most of these results were generated from the 'textmining' component of the search (see Figure 19). However, those papers which were reported under that view of the results will be considered in the discussion of this analysis.


References

He, X.,Khan, A. U., Cheng, H., Pappas Jr D.L., Hampsey M. and Moore, C.L. (2003) Functional interactions between the transcription and mRNA 3′ end processing machineries mediated by Ssu72 and Sub1. Genes Dev. 17, pp. 1030–1042.

Krishnamurthy, S., He, X., Reyes-Reyes, M., Moore, C., and Hampsey, M. (2004) Ssu72 Is an RNA Polymerase II CTD Phosphatase. Molecular Cell 14(3), pp. 387-394.

Krissinel, E., and Henrick, K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Cryst., D60, 2256-2268.

Laskowsk,i R.A., Watson J.D., and Thornton J.M. (2005). Protein function prediction using local 3D templates. J. Mol. Biol., 351, pp. 614-626.

Sun, Z-W. and Hampsey, M, (1996) Synthetic enhancement of a TFIIB defect by a mutation in SSU72, an essential gene encoding a novel protein that affects transcription start site selection in vivo. Mol. Cell. Biol. 16, pp. 1557–1566.

Evolution

Multiple sequence alignment

The psiBLASTp searches show that sequences homologous to Ssu72 are present in many genomes - many of the results are predicted genes in whole genome annotations. Also, the results indicate that some organisms have more than one copy of the gene- for example, Homo sapiens has a match on chromosome 21 (Gene ID 419410) and on chromosome 11 (Gene ID 390031). Other organisms with multiple copies are Pan Troglodytes (chromosomes 11: 745998 and X: 473738) and Canis familiaris (chromosomes 5: 479567 and 21: 485220).

The SwissProt sequences align well, with occasional insertions/deletions (see figure 20). In particular, the Pezizomycotina share two large additional regions in comparison to Drosophila. Four of the yeasts also share a unique region. (The alignment with the Pezizomycotina region is spurious). Debaromyces hasenii also contains two additional regions.

The regions that form the active site (the catalytic residues and the aspartate loop) are highly conserved. Other conserved regions fall within secondary structure features (helices, sheets, hairpin turns).

An alignment of sequences from all the NCBI databases (figure 21) shows a very similar pattern of conserved residues over 78 different organisms. In particular, the key residues in the active site are either invariant or very highly conserved.

The alignment to the eight phosphatases (figure 22) shows that the catalytic residues are the same in the target protein (3fdf) and the phosphatases. However, the aspartate loop in the tyrosine phosphatases is smaller and further along the sequence. Most of these are sequences of tyrosine (or related) phosphatases, with the exception of the acid phosphatase, 2p4u.

Phylogenetic tree

The tree corresponds perfectly to the current taxonomy (figures 23 and 24). The overall grouping is into three branches: Fungi, Amoebozoa and Metazoa. Clear splits in the taxonomy, such as the one between Danio rerio (zebrafish) and the tetrapods, correspond to very high bootstrap values. Low bootstrap values occur when the organisms cannot be ranked based on this protein sequence alone. In some cases, this is because three groups may really be equidistant: for example, Shizosaccharomyces pombe belongs to neither the Pezizomycotina nor to the Saccharomycetales, and the bootstrap value of 56% indicates that a three-way split between the groups would be more appropriate. In other cases, such as the cluster of four yeasts (Candida glabrate, etc.) and the group of tetrapods (Xenopus laevis etc.), the organisms are too similar to be ranked given this highly conserved protein, and the low bootstrap values reflect this.

The tree contains a variety of organisms. The tree does not have any unusual features that need clarification, but it would still be interesting to include more organisms. In particular, plants are not represented at all. However it seems likely from these results that even with additional sequences the tree will still follow known phylogeny.

Structure

Structure determined using XRD. The following images were obtained using RasMol.

PDB 3fdf protein - Secondary Structures

3fdf.jpeg

PDB 3fdf protein - Chains

3fdf 2.jpeg

PDB 3fdf protein - Molecular surface

3fdfms.jpeg




   Protein Structure Database Searching by DaliLite v. 3

The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB).

These are the chains of different molecules that best matched to the Ssu72 RNA polymerase II CTD phosphatase homolog (it is important to notice that the first match corresponds to the protein that is being researched).

PDB ID ... Z rmsd lali nres %id PDB Description

3fdf-A..... 37.3 0.0 191 191 100 PDB MOLECULE: FR253;

3fmv-H... 32.4 0.6 190 190 100 PDB MOLECULE: SERINE PHOSPHATASE OF RNA POLYMERASE II CTD;

1dg9-A... 11.4 2.3 120 157 13 PDB MOLECULE: TYROSINE PHOSPHATASE;

1rxi-A...... 9.9 2.4 109 131 15 PDB MOLECULE: ARSENATE REDUCTASE;


  DaliLite results: Multiple Structure Alignment

Multipleestructuralalignmenta.jpeg


Multiplestructuralalgnmentb.jpeg


  DalaLite results: Superimposed structures

FR253-TYROSINE PHOSPHATASE

3fdf 1dg9.jpeg


FR253-ARSENATE REDUCTASE

3fdf 1rxi.jpeg


FR253-SERINE PHOSPHATASE OF RNA POLYMERASE II CTD

3fdf 3fmv.jpeg



Secondary Structures

FR253

3fdfss.jpeg

SERINE PHOSPHATASE OF RNA POLYMERASE II CTD

3fmvss.jpeg

TYROSINE PHOSPHATASE

1dg9ss.jpeg


ARSENATE REDUCTASE

1rxiss.jpeg




  3fdf vs 1dg9


Drosophila

3fdf.jpg

Tyrosine Phosphatase

1dg9.jpg




  STRING - Known and Predicted Protein-Protein Interactions

Confidence.png

Confidence.jpeg



 Homo sapiens homolog

Structure obtained through Swiss-Model Automatic Modelling Mode

Humanhomolog.jpeg

Superimposition, using Dali server, between Homo sapiens homolog and 3fdf-A

Human-3fdf.jpeg


Structure Alignment

Super1.jpeg

Super2.jpeg


Heading

Abstract | Introduction | Results | Discussion | Method | References