Many Families of Lids for TonB-dependent Transporters inBacteroides

Abstract

Most TonB-dependent transporters inBacteroidesbelong to the SusC family and work with an outer-membrane lipoprotein from the SusD family that functions like a lid. But the best-studied strain,B. thetaiotaomicronVPI-5482, also contains 18 TonB-dependent transporters that are not from the SusC family. We identified six families of putative lids for these transporters. The putative lids are lipoproteins that are encoded next to TonB-dependent transporters, but they are not homologous to SusD. AlphaFold-Multimer predicts that the putative lids bind the outer faces of the corresponding TonB-dependent receptors. Genetic data suggests that members of four of these families are required for the activity of the corresponding TonB-dependent receptors. Overall, of the 18 TonB-dependent receptors that do not belong to the SusC family, we identified alternate lids for nine.

A fast comparative genome browser for diverse bacteria and archaea

“…STRING’s co-occurrence viewer does show that the homologs of BT2172 from other phyla are quite distant, but by a subtle color coding, and this is apparently not taken into account in the automated analysis. In reality, disrupting either BT2172 or BT2173 has similar consequences (Price et al 2023), which confirms that they function together and suggests that the distant homologs of BT2172 from genomes that lack homologs of BT2173 have a different function. But in the absence of the genetic data, the report from STRING that BT2172 has a different distribution than BT2173 would suggest that BT2172 can function on its own, which is misleading.…”

“…Consider the TonB-dependent transporter BT2172. We previously proposed, based partly on comparative genomics evidence, that this transporter functions together with another protein, BT2173, belonging to the uncharacterized family DUF4249 (Price et al 2023). Fast .…”

“…Consider the TonB-dependent transporter BT2172. We previously proposed, based partly on comparative genomics evidence, that this transporter functions together with another protein, BT2173, belonging to the uncharacterized family DUF4249 (Price et al 2023). Fast.genomics shows that these proteins form a conserved operon, and that this subfamily of TonB-dependent transporters is almost always encoded next to a DUF4249 protein, across dozens of genera.…”

A fast comparative genome browser for diverse bacteria and archaea

“…STRING’s co-occurrence viewer does show that the homologs of BT2172 from other phyla are quite distant, but by a subtle color coding, and this is apparently not taken into account in the automated analysis. In reality, disrupting either BT2172 or BT2173 has similar consequences [ 35 ], which confirms that they function together and suggests that the distant homologs of BT2172 from genomes that lack homologs of BT2173 have a different function. But in the absence of the genetic data, the report from STRING that BT2172 has a different distribution than BT2173 would suggest that BT2172 can function on its own, which is misleading.…”

“…Consider the TonB-dependent transporter BT2172. We previously proposed, based partly on comparative genomics evidence, that this transporter functions together with another protein, BT2173, belonging to the uncharacterized family DUF4249 [ 35 ]. Fast .…”