SEA-PHAGES | SecB-like translocase or SecB export protein??

Link to this post \| posted 21 May, 2021 17:43
rlb6	There is no appropriate official function for Gordonia phage Floral_39. There are, however, lots of hits for a SecB-like export protein or translocase. "The Escherichia coli soluble protein SecB is involved in the export of periplasmic and outer membrane proteins." Kumamoto CA. SecB protein: a cytosolic export factor that associates with nascent exported proteins. J Bioenerg Biomembr. 1990 Jun;22(3):337-51. doi: 10.1007/BF00763171. PMID: 2202722. Thoughts about this function? MSKKMSLAEGREAMVRVLQEIQGLKAVRASRIECEALRPLPDSVEEAALVTDVKVSFHASPPYLATFVLYRVCATWGEADEFTDVAEEDQAWRITLEFCADWEVSADAELASEDLRCFAVSQGVMTCHPYARETIQSASVRMGYPPATLDIIRNPLIGDGEIEFED Beckie Bortz 353Kb

Link to this post | posted 21 May, 2021 17:43

There is no appropriate official function for Gordonia phage Floral_39. There are, however, lots of hits for a SecB-like export protein or translocase. "The Escherichia coli soluble protein SecB is involved in the export of periplasmic and outer membrane proteins." Kumamoto CA. SecB protein: a cytosolic export factor that associates with nascent exported proteins. J Bioenerg Biomembr. 1990 Jun;22(3):337-51. doi: 10.1007/BF00763171. PMID: 2202722. Thoughts about this function?

MSKKMSLAEGREAMVRVLQEIQGLKAVRASRIECEALRPLPDSVEEAALVTDVKVSFHASPPYLATFVLYRVCATWGEADEFTDVAEEDQAWRITLEFCADWEVSADAELASEDLRCFAVSQGVMTCHPYARETIQSASVRMGYPPATLDIIRNPLIGDGEIEFED

Beckie Bortz

Link to this post \| posted 03 Jun, 2021 14:17
balish	This protein certainly looks like a relative of SecB, whose actual function is as a chaperone in protein secretion that delivers its unfolded substrates to SecA. Looking quickly at the paper on the structure of SecB from Haemophilus influenzae, I note that the phage protein doesn't conserve all the residues known to be important for the SecB-SecA interaction, so I don't think it's likely that it does what SecB does. Whether it could be a chaperone at all is a good question, and a more difficult one. If anything, I might consider calling it a SecB-related protein, but I'm not too comfortable going beyond that.

Link to this post | posted 03 Jun, 2021 14:17

balish

This protein certainly looks like a relative of SecB, whose actual function is as a chaperone in protein secretion that delivers its unfolded substrates to SecA. Looking quickly at the paper on the structure of SecB from Haemophilus influenzae, I note that the phage protein doesn't conserve all the residues known to be important for the SecB-SecA interaction, so I don't think it's likely that it does what SecB does. Whether it could be a chaperone at all is a good question, and a more difficult one. If anything, I might consider calling it a SecB-related protein, but I'm not too comfortable going beyond that.

Link to this post \| posted 04 Mar, 2022 14:57
NWCiowaSEAPHAGE	balish This protein certainly looks like a relative of SecB, whose actual function is as a chaperone in protein secretion that delivers its unfolded substrates to SecA. Looking quickly at the paper on the structure of SecB from Haemophilus influenzae, I note that the phage protein doesn't conserve all the residues known to be important for the SecB-SecA interaction, so I don't think it's likely that it does what SecB does. Whether it could be a chaperone at all is a good question, and a more difficult one. If anything, I might consider calling it a SecB-related protein, but I'm not too comfortable going beyond that. Hi Mitch! I'm getting HHPred hits from Wrigley_46 to SecB proteins too. The hits are good (probability = 99.8 with 96% coverage). I looked carefully at the sequence of Wrigley_46 and see a D at position 25 (not 20), an E at position 29 (not 24), an I (not L but conservative substitution) at position 78 (not 75) and an E at position 81 (not 77). The Randall et al paper from 2004 also indicates the importance of a C-terminal helix which I have in Wrigley_46. Any thoughts about this one being SecB-like? Enough to justify a functional call or not? I do see in Sala et al 2014 that Mycobacterium have a SecB-like protein (Wrigley is a Gordonia phage). Thanks for your (and anyone else's) help! - sara Edited 04 Mar, 2022 14:58

Link to this post | posted 04 Mar, 2022 14:57

NWCiowaSEAPHAGE

balish
This protein certainly looks like a relative of SecB, whose actual function is as a chaperone in protein secretion that delivers its unfolded substrates to SecA. Looking quickly at the paper on the structure of SecB from Haemophilus influenzae, I note that the phage protein doesn't conserve all the residues known to be important for the SecB-SecA interaction, so I don't think it's likely that it does what SecB does. Whether it could be a chaperone at all is a good question, and a more difficult one. If anything, I might consider calling it a SecB-related protein, but I'm not too comfortable going beyond that.

Hi Mitch! I'm getting HHPred hits from Wrigley_46 to SecB proteins too. The hits are good (probability = 99.8 with 96% coverage). I looked carefully at the sequence of Wrigley_46 and see a D at position 25 (not 20), an E at position 29 (not 24), an I (not L but conservative substitution) at position 78 (not 75) and an E at position 81 (not 77). The Randall et al paper from 2004 also indicates the importance of a C-terminal helix which I have in Wrigley_46. Any thoughts about this one being SecB-like? Enough to justify a functional call or not? I do see in Sala et al 2014 that Mycobacterium have a SecB-like protein (Wrigley is a Gordonia phage).
Thanks for your (and anyone else's) help!
- sara

Edited 04 Mar, 2022 14:58

Link to this post \| posted 04 Mar, 2022 16:20
balish	Hi Sara - When I go to phagesDB, Wrigley_Draft_46 doesn't seem to be the protein you're talking about. It only has 62 amino acids. Can you please let me know how it's currently numbered in that draft annotation, and/or paste the sequence here? -Mitch

Link to this post \| posted 04 Mar, 2022 16:25
NWCiowaSEAPHAGE	Mitch, Sorry! The numbering has changed since we annotated. Here is its sequence: MPVTPGDVTGARIRWRERSAVRHYDGDPEPSYREDVDEEDGPFKLGAEIGRGTDDDDTPIFSVRMKGSFTKPDAQVRIDVEVVFKIDSGEEVDQAFIQKHAMPYVFGYVRGGFTDACRSVGLPGWMIPMVDLAADIQYEDA - sara

Link to this post \| posted 07 Mar, 2022 16:06
balish	Sara, The way I approach this is to use the HHpred output to find the amino acids that correspond to the conserved amino acids in the known structure. In this case, the "invariant" D and E are E and V in Wrigley's protein, and the I and E are a Q and an R in Wrigley. I don't think that bodes well for interacting with SecA. It's also possible that the alignment is incorrect, and that you could find amino acids nearby that could substitute, but I wouldn't personally consider that evidence to be strong. One can also look at other parts of the protein. There's an invariant P in the peptide-binding site (aa 45 in H. influenzae) - nothing in Wrigley lines up precisely, but there are a couple of other P's around - again, not strong evidence. My guess is that this is the product of a gene that shares ancestry with secB, but the protein has probably lost that specific function in favor of something else. Best, Mitch

Link to this post | posted 07 Mar, 2022 16:06

balish

Sara,

The way I approach this is to use the HHpred output to find the amino acids that correspond to the conserved amino acids in the known structure. In this case, the "invariant" D and E are E and V in Wrigley's protein, and the I and E are a Q and an R in Wrigley. I don't think that bodes well for interacting with SecA. It's also possible that the alignment is incorrect, and that you could find amino acids nearby that could substitute, but I wouldn't personally consider that evidence to be strong. One can also look at other parts of the protein. There's an invariant P in the peptide-binding site (aa 45 in H. influenzae) - nothing in Wrigley lines up precisely, but there are a couple of other P's around - again, not strong evidence.

My guess is that this is the product of a gene that shares ancestry with secB, but the protein has probably lost that specific function in favor of something else.

Best,
Mitch

Link to this post \| posted 14 Mar, 2022 15:10
NWCiowaSEAPHAGE	Thanks! Very helpful!

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SecB-like translocase or SecB export protein??