Secondary carrier-type facilitators. Transport systems are included in this category if they utilize a carrier-mediated process to catalyze uniport (a single species is transported by facilitated diffusion in a process not coupled to the utilization of a primary source of energy), antiport (two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy) and/or symport (two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy). These systems are usually stereospecific. Solute:solute countertransport is a characteristic feature of secondary carriers. The dynamic association of transporters and enzymes creates functional membrane transport metabolons that channel substrates typically obtained from the extracellular compartment directly into their cellular metabolism (Moraes and Reithmeier 2012).
The membranes of eukaryotic cells are known to harbor microdomains called lipid rafts. López and Kolter (2010), among others, showed that bacterial membranes contain microdomains functionally similar to those of eukaryotic cells. These membrane microdomains from diverse bacteria harbor proteins involved in signaling and transport. Inhibition of lipid raft formation through the action of zaragozic acid - a known inhibitor of squalene synthases - impaired biofilm formation and protein secretion but not cell viability.
A major limitation to systems-level de-orphanization campaigns is the absence of a structured, language-controlled chemical annotation, but Meixner et al. 2020 described a manual annotation of SLCs. The annotation of substrates, transport mechanism, coupled ions, and subcellular localization for 446 human SLCs confirmed that ~30% of these were still functional orphans and lacked known substrates. Application of a substrate-based ontology to transcriptomic datasets identified SLC-specific responses to external perturbations, while a machine-learning approach based on the annotation allowed identification of potential substrates for several orphan SLCs. The annotation is available at https://opendata.cemm.at/gsflab/slcontology (Meixner et al. 2020).
Subclasses in Class 2 include:
2.A Porters (uniporters, symporters, antiporters). Transport systems are included in this subclass if they utilize a carrier-mediated process to catalyze uniport (a single species is transported either by facilitated diffusion or in a membrane potential-dependent process if the solute is charged), antiport (two or more species are transported in opposite directions in a tightly coupled process, not coupled to a direct form of energy other than chemiosmotic energy) and/or symport (two or more species are transported together in the same direction in a tightly coupled process, not coupled to a direct form of energy other than chemiosmotic energy).
2.B Non-ribosomally synthesized porters. These substances, like non-ribosomally synthesized channels, may be depsipeptides or non-peptide-like substances. They complex a cation in their hydrophilic interior and facilitate translocation of the complex across the membrane, exposing their hydrophobic exterior, by moving from one side of the bilayer to the other. If the free porter can cross the membrane in the uncomplexed form, the transport process can be electrophoretic, but if only the complex crosses the membrane, transport is electroneutral.
2.C Ion gradient-driven energizers. Normally, outer membrane porins (1.B) of Gram-negative bacteria catalyze passive transport of solutes across the membrane, but coupled to eeenergizers,, they may accumulate their substrates in the periplasm against large concentration gradients. These energizers use the ppproton motive force (pmf) across the cytoplasmic membrane, probably by allowing the electrophoretic transport of protons, and conveying conformational change to the outer membrane receptor/porins. Homologous energizers drive bacterial flagellar motility. The mechanism is poorly understood, but these energizers undoubtedly couple proton (H+) or sodium (Na+) fluxes through themselves to the energized process.
2.D Transcompartment Lipid Carriers. Human ORP5 is proposed to function in nonvesicular transfer of low-density lipoprotein-derived cholesterol (LDL-C) from late endosomes/lysosomes to the endoplasmic reticulum (ER) while human ORP8 may modulate lipid homeostasis and sterol regulatory element binding protein (SREBP) activity. Both ORP5 and ORP8 contain an N-terminal Pleckstrin homology (PH) domain (residues 125 - 250), a C-terminal Oxysterol binding protein (OSBP-related) domain, and a C-terminal TMS that localizes ORP5 to the ER. Oxysterol binding proteins comprise a multigene family that is conserved in yeast, flies, worms, mammals and plants. OSBPs and ORPs are involved in the transport and metabolism of cholesterol and related lipids in eukaryotes. OSBP PH domains bind to membrane phosphoinositides and thus play a role in intracellular targeting. They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vesicle transport. PH domains have functions involved in targeting proteins to the appropriate cellular location and have a common fold. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs). PH domains are distinguished by their specific high-affinity binding to PIPs which results in targeting some PH domain proteins to the plasma membrane. PH domains are found in cellular signaling proteins such as serine/threonine kinases, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, and lipid-associated enzymes. They catalyze phospholipid exchange (PI4P for PS) between the plasma membrane and the endoplasmic reticulum (Chung et al. 2015).