SEA-PHAGES | Holin

Link to this post \| posted 28 Jun, 2018 16:59
dbolliva	Currently there is no holin identified in B1 phages? There are a few calls present (Xavier14) but in the homolog DonSanchon 14 the best hit was an HHpred to holin at 75% probability and 33% coverage. Thoughts on this?

Link to this post \| posted 28 Jun, 2018 18:00
dbolliva	After discussing with Welkin, there are no currently approved holin calls in the B1 phages. The gene in question is too far from the lysins combined with the relatively low hit. The gene from DonSanchon does have several predicted transmembrane domains so can be called as a membrane protein

Link to this post \| posted 26 Feb, 2021 18:57
stpage	There are 6 B1 phages in phagesdb calling the holin.

Link to this post \| posted 26 Feb, 2021 18:57
stpage	There are 6 B1 phages in phagesdb calling the holin.

Link to this post \| posted 26 Feb, 2021 19:51
debbie	Hi Shallee, What genes are you referring to? thanks, debbie

Link to this post \| posted 27 Feb, 2021 19:03
cdshaffer	in the database there are 11 phage genes with subcluster B1 they all appear in current pham 48591: `\| phageid \| subcluster \| gene name \| notes \| phamid \| \| BatteryCK \| B1 \| 14 \| holin \| 48591 \| \| Beaglebox \| B1 \| 14 \| holin \| 48591 \| \| DoesntMatter \| B1 \| 15 \| holin \| 48591 \| \| LeeLot \| B1 \| 15 \| holin \| 48591 \| \| Magic8 \| B1 \| 15 \| holin \| 48591 \| \| Megatron \| B1 \| 15 \| holin \| 48591 \| \| Mosaic \| B1 \| 14 \| holin \| 48591 \| \| OliverWalter \| B1 \| 15 \| holin \| 48591 \| \| ProfessorX \| B1 \| 15 \| holin \| 48591 \| \| Trypo \| B1 \| 15 \| holin \| 48591 \| \| Xavier \| B1 \| 14 \| holin \| 48591 \|` for the totally geeky here is the mysql query I used: `> select gene.phageid, phage.subcluster, gene.name as "gene name", gene.notes, gene.phamid from gene join phage on gene.phageid=phage.phageid where phage.subcluster="B1" and gene.notes like "%holin%";` Edited 27 Feb, 2021 19:04

Link to this post | posted 27 Feb, 2021 19:03

cdshaffer

in the database there are 11 phage genes with subcluster B1 they all appear in current pham 48591:


| phageid      | subcluster | gene name | notes | phamid |

| BatteryCK    | B1         | 14        | holin |  48591 |
| Beaglebox    | B1         | 14        | holin |  48591 |
| DoesntMatter | B1         | 15        | holin |  48591 |
| LeeLot       | B1         | 15        | holin |  48591 |
| Magic8       | B1         | 15        | holin |  48591 |
| Megatron     | B1         | 15        | holin |  48591 |
| Mosaic       | B1         | 14        | holin |  48591 |
| OliverWalter | B1         | 15        | holin |  48591 |
| ProfessorX   | B1         | 15        | holin |  48591 |
| Trypo        | B1         | 15        | holin |  48591 |
| Xavier       | B1         | 14        | holin |  48591 |

for the totally geeky here is the mysql query I used:

> select gene.phageid, phage.subcluster, gene.name as "gene name",
gene.notes, gene.phamid from gene join phage on gene.phageid=phage.phageid
where phage.subcluster="B1"
and gene.notes like "%holin%";

Edited 27 Feb, 2021 19:04

Link to this post \| posted 01 Mar, 2021 00:52
debbie	The pfam hits to holin are not great but also not shabby. The typical order of genes is not present in the B1s, so that is also not helpful. However, it is interesting that this gene has 4 transmembrane domains, and the 2 subsequent genes each have 2 transmembrane domains. So I would be inclined to call all three "membrane proteins". Edited 01 Mar, 2021 00:52

Link to this post \| posted 22 May, 2023 13:41
smg366	What are we calling the gene in the B cluster with pfam hits to holin, discussed above?. Phage Inverness gp16 has 95% probability with 40% coverage to holin on HHPRED. HHPRED results in the attachment. There are still only 13 B cluster phages calling holin and the rest calling Hypothetical protein. 157Kb

Link to this post \| posted 22 May, 2023 15:04
debbie	Hi Susan, Holin is one of those gens that is a delight to call, but difficult. it doesn't surprise me that we were not able to call the holin genes historically. Holin genes are many times now callable because of their pfam hits. In this case, that is exactly true. According to deep TMHMM, there are 3 genes directly upstream of the major tail protein that have more than one transmembrane domains. The first of those - the one I think you are pointing to - is a pfam hit to a holin as you describe. I want to call it a holin and the next 2 transmembrane proteins. I would not be surprised if they too are involved in the holin/lysin function for this phage. debbie Here is paper to help! Edited 22 May, 2023 15:12 962Kb

Link to this post | posted 22 May, 2023 15:04

debbie

Hi Susan,
Holin is one of those gens that is a delight to call, but difficult. it doesn't surprise me that we were not able to call the holin genes historically.
Holin genes are many times now callable because of their pfam hits. In this case, that is exactly true. According to deep TMHMM, there are 3 genes directly upstream of the major tail protein that have more than one transmembrane domains. The first of those - the one I think you are pointing to - is a pfam hit to a holin as you describe. I want to call it a holin and the next 2 transmembrane proteins.
I would not be surprised if they too are involved in the holin/lysin function for this phage.
debbie

Here is paper to help!

Edited 22 May, 2023 15:12

Link to this post \| posted 25 May, 2023 12:25
Pollenz	We have use a Bioinformatic approach to identify several phage clusters that have a distal holin-like gene cassette that are not associated with the lysins. This type of organization can be observed in the B1, B2, B3, B5, B9, DR and DO phages. Most of the cassettes have four different TM genes with a 4-4-4-1 configuration and in many cases all these genes have a 4bp overlap to each other. We have bioinformatically looked at all of the pham members for all of these distal holin-like genes and CAN FIND THEM DIRECTLY DOWNSTREAM of lysins in DD, EP, DV, DG1, DK CZ2, DB, CS4, CV, CY and CZ7. This clearly validates that they are likely functioning in lysis. I have enclosed an colorful analysis based on the 4 genes in the DR Phage CaiB. Each color represents a protein in the same pham. In the case of your B1 phages, note that phages in the DD cluster have both 4TM genes directly downstream of a split lysin followed by a 1TM gene. Based on our wet lab recent work, it is likely that ALL of the TM genes are holins (including the 1TM that may be the most important one. DATA IN PREP but presented at 2023 Phages Conference). Note that the majority of these multi-TM gene cassettes have a terminal 1TM gene. See our PLOSONE paper as well for a comprehensive analysis of these types of TM cassettes. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0276603 RS Pollenz Edited 25 May, 2023 15:43 1011Kb

Link to this post | posted 25 May, 2023 12:25

Pollenz

We have use a Bioinformatic approach to identify several phage clusters that have a distal holin-like gene cassette that are not associated with the lysins. This type of organization can be observed in the B1, B2, B3, B5, B9, DR and DO phages. Most of the cassettes have four different TM genes with a 4-4-4-1 configuration and in many cases all these genes have a 4bp overlap to each other.

We have bioinformatically looked at all of the pham members for all of these distal holin-like genes and CAN FIND THEM DIRECTLY DOWNSTREAM of lysins in DD, EP, DV, DG1, DK CZ2, DB, CS4, CV, CY and CZ7. This clearly validates that they are likely functioning in lysis. I have enclosed an colorful analysis based on the 4 genes in the DR Phage CaiB. Each color represents a protein in the same pham.

In the case of your B1 phages, note that phages in the DD cluster have both 4TM genes directly downstream of a split lysin followed by a 1TM gene. Based on our wet lab recent work, it is likely that ALL of the TM genes are holins (including the 1TM that may be the most important one. DATA IN PREP but presented at 2023 Phages Conference). Note that the majority of these multi-TM gene cassettes have a terminal 1TM gene. See our PLOSONE paper as well for a comprehensive analysis of these types of TM cassettes. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0276603

RS Pollenz

Edited 25 May, 2023 15:43

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