| Level in hierarchy | Protein(s) | Module assignment | Dependence (what it requires for TZ localization) | Role in TZ |
|---|---|---|---|---|
| 1 (most upstream) | MKS-5 / RPGRIP1L | Master TZ assembly factor / scaffold linking MKS and NPHP branches | Localizes independently of CEP-290; required for localization of essentially all tested TZ proteins, including CEP-290, MKS-module, and NPHP-module proteins (pqac-00000018, pqac-00000022, pqac-00000024, pqac-00000031) | Foundational organizer of TZ formation; establishes TZ ultrastructure, supports Y-link formation, and helps create the ciliary zone of exclusion/barrier (pqac-00000022, pqac-00000024, pqac-00000028, pqac-00000032) |
| 2A | NPHP-1, NPHP-4 | NPHP module | Assemble in the MKS-5-dependent branch; localization does not require CEP-290 (pqac-00000019, pqac-00000020, pqac-00000022) | Parallel TZ branch that works redundantly with the MKS branch to seal the ciliary compartment, maintain membrane attachments, and support ciliogenesis/barrier function (pqac-00000020, pqac-00000026, pqac-00000028, pqac-00000029) |
| 2B | CEP-290 | CEP-290-dependent MKS assembly branch | Requires MKS-5 for TZ localization; acts downstream of MKS-5 and upstream of MKS-module proteins (pqac-00000018, pqac-00000019, pqac-00000020, pqac-00000022) | Core assembly factor for the MKS pathway; required for Y-links/apical ring integrity and ciliary gate function, and specifically recruits/organizes MKS-module proteins at the TZ (pqac-00000017, pqac-00000018, pqac-00000019) |
| 3 (core MKS layer) | MKS-1, MKSR-1/B9D1, MKSR-2/B9D2, MKS-2/TMEM216, TMEM-231 | Core MKS module | Require CEP-290 and MKS-5 for TZ localization; core members are interdependent with one another for proper localization (pqac-00000017, pqac-00000018, pqac-00000020, pqac-00000023) | Principal MKS gate components; organize the membrane-proximal barrier, support TZ ultrastructure, and are necessary for proper ciliary compartmentalization/gate function (pqac-00000017, pqac-00000020, pqac-00000025, pqac-00000029) |
| 4 (peripheral MKS layer) | TMEM-17, TMEM-67, TMEM-218, TMEM-237 | Peripheral MKS module | Require CEP-290, MKS-5, and intact core MKS proteins for TZ localization; do not control localization of core MKS proteins (pqac-00000017, pqac-00000020, pqac-00000023) | Downstream effectors/accessory MKS components that elaborate TZ composition and contribute to mature gate/barrier function rather than initiating core assembly (pqac-00000017, pqac-00000020, pqac-00000029) |


*Table: This table summarizes the hierarchical assembly of the C. elegans ciliary transition zone, placing MKSR-1/B9D1 within the CEP-290-dependent core MKS module. It is useful for understanding which proteins act upstream versus downstream in building the transition-zone barrier.*