Rep15 interacts with several Rab GTPases and has a distinct fold for a Rab effector

Abstract

In their GTP-bound (active) form, Rab proteins interact with effector proteins that control downstream signaling. One such Rab15 effector is Rep15, which is known to have a role in receptor recycling from the endocytic recycling compartment but otherwise remains poorly characterized. Here, we report the characterization of the Rep15:Rab15 interaction and identification of Rab3 paralogs and Rab34 as Rep15 interacting partners from a yeast two-hybrid assay. Biochemical validation of the interactions is presented and crystal structures of the Rep15:Rab3B and Rep15:Rab3C complexes provide additional mechanistic insight. We find that Rep15 adopts a globular structure that is distinct from other reported Rab15, Rab3 and Rab34 effectors. Structure-based mutagenesis experiments explain the Rep15:Rab interaction specificity. Rep15 depletion in U138MG glioblastoma cells impairs cell proliferation, cell migration and receptor recycling, underscoring the need for further clarification of the role of Rep15 in cancer.

The genome of the pygmy right whale illuminates the evolution of rorquals

“…For five out of six candidate genes, we found evidence in the literature for a correlation between expression patterns and cancer development (Table 2 [ 66 – 70 ]). Furthermore, we found more detailed functional descriptions for two of these genes: first, the C-type lectin domain family 2 member B (CLEC2B/AICL), which is a protein encoded by the natural killer (NK) gene complex proximal CD69 [ 71 ]; and second, the RAB15 effector protein (REP15), which together with its associated Rab GTPase controls the flow of transport vesicles in the brain [ 69 ]. The ortholog with the highest divergence between Ka and Ks in all three pairs is so far uncharacterized in humans (LOC124907494/LOC124905498) and has only been characterized as “proline-rich” in, e.g., cattle (LOC113892484).…”

“…Sorted by Ka/Ks ratio. Concerning publications: [ 66 – 70 ] Symbol HGNC Orthogroup Description Literature Ka/Ks p -val LOC124907494/LOC124905498 - OG0018750 Uncharacterized (basic salivary proline-rich protein 1-like in Bos indicus ) - 8.19 0.001 C6orf15 (STG) 13,927 OG0018717 Unknown function (expressed in various types of cancer) Xiong et al, (2022) [ 66 ] 2.74 0.165 MGAT4EP 49,418 OG0018311 Pseudogene in human (upregulates the expression of FOXM1 in breast cancer) Sun et al, (2021) [ 67 ] 2.06 0.474 CLEC2B/AICL 2053 OG0018915 Associated with natural killer cells, expressed in various types of cancer Li et al, (2022) [ 68 ] 1.95 0.532 REP15 33,748 OG0018380 Involved in vesicular trafficking, potentially involved in various types of cancer Rai et al, (2022) [ 69 ] 1.67 0.403 C22orf46 26,294 OG0017847 Unknown function (oncogene in adreno-cortical carcinoma) Li et al, (2020) [ 70 ] 1.43 ...…”

“…The proline-rich protein LOC124907494 (human) is to our knowledge unknown to cancer research and shows the most non-synonymous mutations in large baleen whales, therefore, representing an interesting target for further research. Within our six selected genes, two were already described in greater detail, namely CLEC2B and REP15 [ 68 , 69 ]. CLEC2B is a member of the C-type lectin domain family 2 and was formally described as activation-induced C-type lectin (AICL) [ 71 ].…”

“…Its positive selection in large-bodied baleen whales might represent adaptations to this complex to better control the activation and migration of lymphocytes when encountering cancer. REP15 is the effector of the Rab15 GTPases which are assumed to control vesicular traffic in neuronal tissue [ 69 ], a function possibly involved in the adaptions to increase body size. However, a multi-omics analysis also suggested REP15 as a colorectal cancer-specific driving gene [ 86 ], and it was shown to interact with other Rab proteins [ 69 ] of which many are discussed to be involved in tumorigenesis because of its potential role in signal transduction to stimulate progression and invasion into other areas [ 87 ].…”

“…Differentiating between the individual pairs we found: 89 (bowhead/pygmy right), 95 (fin/minke), and 74 (blue/rice) positively selected orthologs, respectively. Six of those genes were found to have an elevated non-synonymous substitution rate in all three pairs (Table 2 [66][67][68][69][70]) that were further functionally specified by BLAST. For five out of six candidate genes, we found evidence in the literature for a correlation between expression patterns and cancer development (Table 2 [66][67][68][69][70]).…”