# Gene transcriptions/Boxes/Fs

"The F-box is a protein motif of approximately 50 amino acids that functions as a site of protein-protein interaction."

## Gene transcriptions

"The F-box of Elongin A binds Elongin C (El C). The association of Elongins B and C with A increases Elongin A transcriptional activity."
"SCF complexes generally recognize substrates after they are phosphorylated on specific epitopes [10]. Phosphorylation is one of the major mechanisms used by cells to rapidly transduce signals. SCF complexes are therefore ideal for dynamic processes that require an abrupt change to be made irreversible (at least in the short term) via the degradation of key proteins. Examples of such processes are cell-cycle phase transitions - during which the cell-cycle regulators that were required for the previous phase are degraded as the cell enters the new phase - and shifts in transcription that last for a longer time period than otherwise because a transcriptional inhibitor is degraded. There is a wide variety of SCF targets that include cell-cycle regulators, for example, G1-phase cyclins, cyclin-dependent kinase inhibitors, DNA replication factors, and transcription factors that promote cell-cycle progression, as well as non-cell-cycle functions, such as a cytoskeletal regulator, cell-surface receptors, transcription-factor inhibitors, and non-cell-cycle transcription factors (Table 2)."
"Second, Elongin A, the transcriptionally active subunit of the Elongin (SIII) complex - which facilitates transcription elongation by RNA polymerase II [16] - is an F-box protein (Figure 2c). Elongin A was isolated by virtue of its ability to increase the catalytic rate of transcript elongation by RNA polymerase II in vitro [16]. Binding of the other components of the complex, Elongin B and C, increases the specific activity of Elongin A. The F-box motif of Elongin A is in the smallest region shown to be sufficient for Elongin A to bind Elongin C in both yeast and humans [17,18]. Elongin C has homology to Skp1; the F-box-Elongin C interaction may therefore be evolutionarily conserved."
"In order to examine the factors involved in regulating telomere length homoeostasis, Liu et al.$^{25}$ carried out a genome-wide screen of deletion mutations that impacted telomere length in S. pombe$^{25}$. Deletion of 168 genes was found to alter telomere length, with four causing ‘very short’ telomeres (>150 bp shorter than wild type). These were est1, trt1 and ccq1, which are essential for telomerase activity, and pof8, of unknown function. Pof8 is a putative F-box protein, which bind to Skp1 and Cullin to form an SCF E3 ubiquitin ligase complex$^{26}$. Previous studies identified Pof8 as a Skp1 binding protein but the association with Cullin was not determined$^{27,28}$, implying a function distinct from a canonical F-box protein. Here we redefine Pof8 as an RNA-binding protein of the ancient LARP7 family (Laribonucleoprotein domain family member 7 or La-related protein 7) and thus rename it Lar7. LARP7 proteins are characterised by an N-terminal RNA-binding domain termed a La-motif and two RNA-recognition motifs (RRMs). LARP7 proteins associate with non-coding RNAs transcribed by RNA polymerase III, which have a hallmark 3′-UUU-OH tag$^{29}$. Here we report that Lar7 interacts with TER1 and plays a crucial role during its biogenesis. Lar7 stabilises the interaction between TER1 and the Lsm2–8 complex and facilitates assembly with Trt1. Loss of Lar7 leads to disassembly of telomerase and exosomal degradation of TER1, resulting in impaired telomerase activity and maintenance of very short telomeres. Further, we report a high degree of conservation between Lar7 and both the human protein hLARP7 and Tetrahymena thermophila telomerase RNA-binding protein p65. In human cells, loss of hLARP7 has recently been shown to cause telomere shortening$^{30}$. Thus, LARP7-familiy proteins are universally crucial for telomere maintenance."
"Lar7 is a member of the LARP7 RNA-binding protein family. In order to assess the function of Lar7 in telomere biology, we first analysed its predicted structure for key domains or moieties that may allude to its function. Using the bioinformatics tool HHpred (homology detection and structure prediction by HMM-HMM) and the Protein Homology/Analogy Recognition Engine v2.0 (Phyre2)$^{33,34}$, we identified two likely RNA-recognition motifs (RRMs), which have the format β1-α1-β2-β3-α2-β4, in four fission yeast species [...]. Additionally, we identified structural similarity between Lar7 and the human protein hLARP7 (La-related protein 7 or La ribonucleoprotein domain family member 7), which is part of the wider LARP7 family of non-coding RNA-binding proteins$^{35}$. Remarkably, a well-described member of this family and orthologue of hLARP7 is the telomerase-binding protein p65 in ciliate T. thermophila. All LARP-family proteins (including hLARP7 and p65) have a conserved N-terminal La-motif followed by an RRM (together termed the ‘La-module’) and a second RRM toward the C-terminus [...]. The alignment of S. pombe Lar7 with p65 and hLARP7 and a comparison of Lar7 with the published structures of hLARP7 and p65$^{36–38}$ revealed considerable sequence and structural similarity between the three proteins [...]. The reported secondary structure of a La-motif is α1-β1-α2-α3-β2-β339. According to the HHpred analysis, the N-terminus of S. pombe Lar7 corresponds to this predicted structure (amino acids 64–138), preceding RRM1 (amino acids 148–230). We have therefore assigned this region a La-motif. Interestingly, the domain assigned as an F-box in Lar7 (amino acids 66–106$^{27,28}$) lies within the La-motif. Due to this striking conservation and the criteria defining LARP7 family proteins$^{29}$, in addition to the function of Lar7 in telomerase RNA binding (defined in this report), we concluded that the annotated Pof8 is a member of the LARP7 family and accordingly renamed it Lar7 (La-related protein 7)."