PAMGO ML modifications

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Biological Process

Proposed term modifications

(only items to be changed are shown)

type I protein secretion system ; GO:0030253

Synonyms

  • broader: ABC translocator


type II protein secretion system ; GO:0015628

Synonyms

  • exact: type II protein (Sec) secretion system
  • exact: T2SS
  • exact: main terminal branch
  • exact: MTB
  • related: Sec-dependent secretion system [sensu bacteria]
  • related: general secretion pathway [sensu bacteria]
  • related: general secretory pathway [sensu bacteria]

Definition:

  • A bacterial system for secretion of proteins across the outer membrane using a dedicated secretion apparatus involving multiple proteins. Proteins using this pathway are first translocated across the inner membrane via the Sec (general secretory) or TAT pathways.


type III protein secretion system ; GO:0030254

Synonyms

  • exact: TTSS
  • exact: T3SS


type IV protein secretion system ; GO:0030255

Synonyms

  • exact: T4SS


Type IV pilus dependent-motility ; GO:0043107

(primary term name was switched with that of a synonym, since I think its better to not use acronyms (aka TFA) as the primary term name)

Synonyms:

  • exact: TFP-dependent motility


pilus biogenesis ; GO:0009297

I have tweaked the definition of the following term so that individual pili types (such as Type IV pili) can be children. As the definition was previously written, it implied that all children had to be involved in conjugation, adherence and so on…

Synonyms:

  • exact: pilus biosynthesis

Definition:

  • The assembly of a pilus, a short filamentous structure on a bacterial cell, flagella-like in structure and generally present in many copies. Pili are variously involved in transfer of nucleic acids, adherence to surfaces, and formation of pellicles Is required for bacterial conjugation and plays a role in adherence to surfaces (when it is called a fimbrium), and in the formation of pellicles.


Proposed new terms

Sec protein translocation system (sensu Bacteria)

  • Child of “Intracellular protein transport” GO:0006886
  • Child of “Protein insertion into membrane” GO:0051205

Synonyms:

  • exact: Sec protein export system
  • related: general secretion pathway [sensu Bacteria]
  • related: general secretory pathway [sensu Bacteria]
  • related: general export pathway [sensu Bacteria]

Definition:

  • A system for translocation of unfolded proteins across the bacterial cytoplasmic membrane, involving SecA,D,E,F,G,Y and YajC. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2). Sec-translocated proteins are subsequently secreted via the type II, IV, or V secretion systems.


TAT protein translocation system (sensu Bacteria)

  • Child of “Intracellular protein transport” GO:0006886

Definition:

  • A system for translocation of folded proteins across the bacterial cytoplasmic membrane, generally involving three integral membrane proteins. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2). Proteins tanlocated by the Tat pathway may be subsequently secreted via the type II secretion systems.


Type IV pilus biogenesis

  • Child of “pilus biogenesis”: GO:0009297

Synonyms:

  • exact: Type IV fimbria assembly
  • exact: Type IV fimbria biogenesis
  • exact: Type IV fimbriae assembly
  • exact: Type IV fimbriae biogenesis
  • exact: Type IV fimbrial assembly
  • exact: Type IV fimbrial biogenesis
  • exact: Type IV fimbrium assembly
  • exact: Type IV fimbrium biogenesis
  • exact: Type IV pilus biosynthesis
  • exact: TFP biogenesis
  • exact: Type 4 pilus biogenesis

Definition:

  • The assembly of a Type IV pilus, composed of a pilus fiber and approximately ten proteins at its base; Type IV pili play a role in cell motility, adherence to substrates, and aggregation


Cellular Component

Proposed term modifications

(only items to be changed are shown)

type I protein secretion system complex ; GO:0030256

Synonyms:

  • broader: ABC translocator complex
  • Change from being child of GO:0044459 “plasma membrane part” to child of GO:0044464 “cell part” (The decision to move large secretion complexes directly to “cell part” GO:0044464 was made with Michelle prior to the July meeting)


type II protein secretion system associated complexes ; GO:0015627

  • Change from being child of GO:0044459 “plasma membrane part” to child of GO:0044464 “cell part”

Synonyms:

  • exact: type II protein (Sec) secretion system associated complexes
  • exact: T2SS associated complexes
  • exact: main terminal branch
  • exact: MTB
  • related: Sec-dependent secretion system associated complexes [sensu bacteria]
  • related: general secretion pathway associated complexes [sensu bacteria]
  • related: general secretory pathway associated complexes [sensu bacteria]

Definition:

  • A set of complexes composed of two or more of the approximately 15 proteins that together carry out Type II protein secretion across the outer membrane, following transport across the inner membrane by the Sec or TAT pathways


Request to move mis-annotated genes out of GO:0015627

  • Several genes using the three letter designation Sec or Yaj are presently annotated to GO:0015627. These need to be moved to “Sec complex” GO:0031522


type III protein secretion system complex ; GO:0030257

  • Change from being child of GO:0044459 “plasma membrane part” to child of GO:0044464 “cell part”

Synonyms

  • exact: TTSS complex
  • exact: T3SS complex


Sec complex (sensu Bacteria) ; GO:0031522

  • Change from being child of GO:0044459 “plasma membrane part” to child of GO:0044464 “cell part”

Definition:

  • A transmembrane protein complex involved in the translocation of proteins across the cytoplasmic membrane. In Gram-negative bacteria, Sec-translocated proteins are subsequently secreted via the type II, IV, or V secretion systems. Sec complex components include SecA,D,E,F,G,Y and YajC. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2).


Request to move mis-annotated genes out of GO:0015628

  • Several genes using the three letter designation Sec or Yaj are presently annotated to GO:0015628. These need to be moved to “Sec protein translocation system (sensu Bacteria)” (see above) when a GO term has been established


Proposed new terms

TAT protein translocation system complex (sensu Bacteria)

  • Child of “plasma membrane part” GO:0044459

Definition:

  • A complex of three proteins integral to the bacterial cytoplasmic membrane involved in translocation of folded proteins across the bacterial cytoplasmic membrane. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2).


type IV protein secretion system complex

  • Child of “cell part” GO:0044464

Synonyms:

  • exact: T4SS complex

Definition:

  • A complex of proteins related to those involved in bacterial DNA conjugative transfer, that permits the transfer of nucleoprotein DNA conjugation intermediates or proteins into the extracellular milieu or directly into host cells. In general the type IV complex forms a multisubunit cell-envelope-spanning structure composed of a secretion channel and often a pilus or other surface filament or protein(s)


Pilus and fimbria terms in GO

Right now, GO has a number of fimbrial terms in the cellular component ontology.

There are two problems with this:

  1. It was decided that the term pilus should be primary to fimbria
  2. These terms are all children of intracellular organelle (GO:0043229) instead of cell projection part (GO:0044463) where they more logically belong (as a sibling of other projections like flagella)

I don’t know the proper protocol, but I favor:

  1. adding the two new terms below
  2. transferring annotation under fimbrium GO:0009289 to pilus part (below)
  3. obsoleting the following terms:
  • fimbrium GO:0009289
  • fimbrial shaft GO:0009418
  • fimbrial tip GO:0009419


Proposed new terms

pilus part

  • Child of “cell projection part” GO:0044463

Synonyms:

  • exact: fimbriae

Definition:

  • Any constituent part of a pilus, a short filamentous structure on the surface of bacterial cell variously involved in nucleic acid transfer, motility, and adherence to substrates


Type IV pilus part

  • Child of “pilus part” (see above)

Synonyms:

  • exact: type IV fimbriae
  • exact: TFP part
  • exact: type 4 pilus part

Definition:

  • Any constituent part of a Type IV pilus, a short filamentous structure on the surface of a bacterial cell distinguished from other pili by post-translational N-methylation of the pilin monomers


Other questions

Can adhesion to host (GO:0044406) be a child of cell-substrate adhesion (GO 0031589)?

Amelia

I don't think so, unless an organism is a kind of substrate. Perhaps we should have a 'cell-organism surface adhesion' term?

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