Biochemistry Research Paper

Introduction

The Transcription elongation factor B, polypeptide 1 is a protein variant that in the species Homo sapiens is encoded by the TCEB1 gene also referred to as SIII or eloC (National Center for Biotechnology Information (NCBI), 2015, sec. 1). Structurally, the SIII Complex is a heterotrimeric compound composed of three elongins sub-units – elongins A and A2 (110kD), B (18kD), and C (kD). However, further analysis divulges that elongin C protein is a subunit of the transcription factor B framework (otherwise referred to as elongin SIII complex) (GeneCards, 2014, sec. 1). Functionally, the SIII compound purpose is the activation of the elongation RNA polymerase II process. To accomplish this task, the SIII compound triggers the suppression of the polymerase transient pausing located at various sites within the transcription units. In this particular process, the elongins B (600787) and C (TCEB1) functions as regulatory subunits, whereas the elongin A (600786) sub-unit plays the transcriptionally active component of the SIII compound (Bocchini, 2003, sec. 1; Conaway, 1996, sec. 1).
As part of its functional role, the capability of elongin A2 in forming stable complexes with the other elongins (B and C) is explicitly articulated while in the human testis. On the other hand, the elongins B and C are bound to the von Hippel-Lindau (VHL) tumor suppressor protein during the transcription elongation thus inhibiting the process (Neckers, Christopher, Ricketts, & Linehan, 2013, sec. 1). Additionally, a number of scientific studies have shown that the human gene TCEB1 is capable of interacting with both the TCEB2 gene and the von Hippel-Lindau tumor suppressor protein. In its human biological functioning, the TCBE2 gene encodes the Transcription elongation factor B polypeptide 2 protein. Also referred to as the pVHL, the Von Hippel–Lindau tumor suppressor protein is programmed by the VHL gene in the sapiens species. However, multiple studies shows that the human Von Hippel–Lindau disease is caused primarily by mutational incidences on the VHL gene (Duan et al. 1995 and Kibel et al. 1995 as cited in Bochini, 2003, sec. 2).

The Structure and Expression of the TCEB1 Gene

There is a generalized consensus that cells in multicellular entities are genetically homogeneous despite the fact they are both functionally and structurally heterogeneous. This observable dissimilarity is due to differential gene expression (Bird & Jaenisch, 2003, sec. 1). Concerning TCEBI manifestation, diverse literature defines genes expression as the process in which the sequence alignments of a gene are transformed into a mature gene product or by-products (proteins or RNA). This process includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA strand (for protein-coding genes) and the subsequent translation of that mRNA into proteins. (AmiGO2, 2015).
However, additional protein processing events may be included in the gene expression process when the formation of an active form of a protein product from an inactive precursor form is required. According to UniProtKB and Swiss-Prot, the TCEB1 gene has a structural size of 112 amino acids 12473 Da (GeneCards, 2014, sec. 4). Supplementary investigations show that TCEB1 is composed of several sub-units structurally bonded into a single structural strand such as the Heterotrimeric combination of the A (A1, A2 or A3), B, and C elongin subunits (Tsuchiya, Ised, & Hino, 1996, sec. 2). The appendix section contains a simplified illustration of the TCEBI gene labelled diagram (c).

TCEB1 Cell location, Signal Sequencing, and Post-Translational Modifications (PTM)

According to numerous scientific literatures, the Homo sapiens transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C) is located on Chromosome 8, NC_000008.11 (7394513873972287, complement) (NCB1; Ensembl, 2015). Data from GeneCards (2014) shows that the human TCEB1 gene has “ten transcripts (splice variants), 77 different orthologues and is classified under the 2 Ensembl protein families. The TCEB1 protein is further associated with 19 different human phenotypic traits” (Ensembl, 2015). Further analysis exposes that the human TCEB1 gene exhibits known protein binding process as part of its biological human functioning. Defining protein binding process as the selective non-covalent interaction between the genes and any protein or protein complex, information from AmiGO2 (2015) shows that the TCEB1 gene interacts with proteins in a number of ways. Available data on the same divulges that TCEB1 interacts with 130 markers (Mouse Genome Informatics (MGI), 2015, sec. 9). Those cellular proteins known to interact with TCEB1 include the alpha-2 macroglobulin receptor-associated protein and the protein degradation tagging activities. In these interactions, a complex protein is portrayed as a compound of two or more proteins that may include other non-protein molecules (Neckers et al. 2013, sec. 1).
Regulation of the TCEBI gene expression is well documented with data showing that it is most susceptible to environmental regulation mechanisms. In this process, the cell uses multiple external factors to either increase or decrease the production of specific gene products mainly protein components or various forms of Ribonucleic Acids (RNA). For the TCEBI gene, such significant environmental factors include external temperature variations, fluctuating oxygen levels, and the varying degrees of the cellular pH conditions.

Functions and interactions of the *600788 protein

A glimpse into the functional interactions of the *600788 protein in this place referred to as the Transcription elongation factor B; polypeptide 1 protein shows innumerable significant roles of this protein in the human body (Bocchini, 2003). Also called elongin C, the TCEB1 SIII is a transcription factor that “increases the RNA polymerase II transcription elongation past the cellular template-encoded arresting sites” (PhosphoSitePlus, n.d.). As partly illustrated in the appendix the diagram (a) and Table one shows the transcriptional activity of the active Subunit A is heightened by the structural bound it has to the dimeric complex of the elongin BC complex. More scientific evidence show that this protein is located in the human chromosomal location at the 8q21.11 site, and is classified under the protein group type known as the Transcription initiation complexes. The biological functions of this protein nonetheless revolve around protein binding and protein complex binding processes. Consequently, the Transcription elongation factor B, polypeptide 1 protein plays significant roles in the human biological processes. Diagram (b) in the appendix shows a simplified TCEB13D illustration.
As one of its numerous functions, TCEB1protein regulates the transcriptional processes from the RNA polymerase II promoter while initiating the ubiquitin-dependent protein catabolic processes (Neckers et al. 2013, sec. 1). Secondly, the protein enhances cellular viral reproduction process and oversees the active regulation of RNA elongation from RNA polymerase II promoter. However, its primary role is facilitating gene expression in humans (PhosphoSitePlus, n.d.).

Human Diseases associated with mutations in TCEB1 gene

Multiple scientific studies show that there are several conditions relevant to the human TCEB1 gene. For instance, a study conducted by Kobayashi et al. (2005) showed that Ubiquitination of APOBEC3G by the HIV-1 Vif-Cullin5-Elongin B-Elongin C complex is essential for Vif function (sec. 1). In this particular study, the research findings suggested that the sequences outside the elongin C binding box of the SIII complex might function as a nuclear export domain, potentially providing a unique role in this area of VHL structure frequently mutated in renal cell carcinoma. Other studies using cDNA microarrays found that there were a considerable overexpression and amplification of Elongin C in both breasts and prostate cancer (PCa) cells (Agell & Hernández, 2012, para 2; Porkka, Saramäki, Tanner, & Visakorpi, 2002). Conclusively, analysis from these TCEB1 mutations preferentially involved residues that directly bind to elongin C and alter the conformation of pVHL such that the binding process to elongin C is at least partially diminished. However, of concern of the known mutational diseases of the TCEB1 gene in humans is the Von Hippel–Lindau syndrome (VHL) (Tsuchiya, Ised, & Hino, 1996, sec. 1). The Appendix section labelled Table 2 highlights some of the noteworthy diseases linked to TCEBI.

VHL Functions

Scientifically, VHL is an abbreviation that stands for “Von Hippel-Lindau tumor suppressor” gene (Genetics Home Reference, 2012, para. 2). In normal circumstances, this gene works to provide cellular instructions for the manufacture of the VCB-CUL2 protein complex. As part of its biological function, the VCB-CUL 2 protein complex facilitates cellular destruction of unwanted cell components. Of primary concern, however, is the influence of VCB-CUL2 protein complex on HIF via modifications on the hypoxia-inducible factor 2-alpha (HIF-2α) (Lifshitz & Plotkin, 2007, p. 258). This is because, other than HIF controlling the body's aptitude adaptation to varying intracellular oxygen conditions, it also regulates the manufacturing of numerous genes comprehensively linked to cell division. Such important genes include the vascular endothelial growth factor (VEGF), the transforming growth factors (TGF-a and TGF-b), and the platelet-derived growth factor (PDGF). Subsequently, multiple studies indicate that the mutations in the VHL gene accelerates the emergence, growth, and development of tumors.
The Von Hippel-Lindau (VHL) syndrome is a human and inheritable disorder that is mainly characterized by the formation of various forms of tumors and fluid-filled sacs (cysts) in many different parts of the body (Lifshitz & Plotkin, 2007, p. 257). Tumors associated with VHL may be either noncancerous or cancerous with signs and symptoms occurring throughout the patient life. Studies also show that VHL is an autosomal inherited tumor syndrome with VHL type I or VHL type II tumors. However, the most common tumors are phaeochromocytoma and central nervous system (CNS) haemangioblastomas (Genetics Home Reference, 2012, para. 2). Further epidemiological information reveal that VHL syndrome is associated with multiple visceral lesions such as pancreatic and renal cysts and epididymal cystadenoma. The underlying genetics of this disease stems from mutations or deletions in the tumor suppressor gene usually mapped on the short arm of chromosome 3 (3p25). In this particular chromosomal locale, the gene coding sequence typically contains three exons and two major isoforms of messenger ribonucleic acid (mRNA). Therefore, when there is a loss, total, or partial inactivation of the wild-type allele in this section of the cell, tumor formation is in most cases guaranteed (Lifshitz & Plotkin, 2007, p. 258).
In addition, there is a generalized agreement among the scientific community that pVHL plays a significant part in tumor development through the ubiquitinylation and degradation of HIF1α. This is because evidences show that it degrades the HIF in the presence of sufficient oxygen (Frantzen, Links, & Giles, 2012). Thus, cancerous tissues lacking functional p VHL, overproduce HIF, that then targets identified cell proteins such as VEGF. The cancerous tissues also transform the growth-factor alpha into its active state resulting in the uncontrolled proliferation of hamartomatous blood vessels in individuals with VHL mutation (Genetics Home Reference, 2012, para, 5). In its normal biological operations, “elongin C combines with pVHL to form a complex compound that further binds with cullin-2, elongin B, and Rbx1” as shown in the diagram (d) in the appendix. Subsequently, the VHL protein binds to the hydroxylated HIF1α and marks it for degradation. However, under hypoxic conditions, HIF1α is not hydroxylated and pVHL fails bind thus leading to the accumulation of HIF1α subunits in the cell. Additionally, the HIF1α forms heterodimers with HIF1β, which activates the transcription of a variety of hypoxia-inducible genes (such as VEGF, TGFα, and PDGFβ). Correspondingly, when pVHL mutates, HIF1α subunits tends to accumulate in the cells, resulting in tumor neovascularization, a symptomatic characteristic of VHL disease (Kaelin, 2002, as cited in Frantzen, Links, & Giles, 2012).
The treatment of VHL in most patients especially those exhibiting symptoms of pancreatic lesions usually require surgical operations. However, the frequent multiplicity of the VHL tumors and the presence of other organs involvements often curtails therapeutic decisions. Consequently, a multidisciplinary approach is required to optimize the VHL treatment. Nonetheless, early diagnosis is essential. On the other hand, recent advancements in medicine reveal that VHL morbidity and mortality are improving because such developments have made it possible to diagnose and treat VHL associated tumors at its early stages. For instance, stereotactic radiotherapy has been successful for individuals with surgically inaccessible brain lesions. Other treatment procedures include cryotherapy and laser therapy for retinal angiomas.

Recently Published Research about the TCEB1 gene

In recent scientific developments, there has been an upsurge in the number of scientific research that attempts to shade light on the biochemical nature of human genes. One such gene that has received significant attention is the human TCEB1 gene. For instance, one such study is the “New insights into von Hippel-Lindau Function Highlighted by investigation of the trichloroethylene-induced p.P81S Hotspot Mutation” published by the Journal of National Cancer Institute. In this particular publication, the authors investigate the nature of the VHL gene, the TCEB1 gene mutations, and the Biallelic inactivation of VHL. Even though the paper is mainly centered on trichloroethylene-induced p.P81S Hotspot Gene Mutation, it provides relevant scientific information on the functional as well as the structural components of the TCEB1 gene. It also highlights some of the common disorders associated with the gene mutations (Neckers et al. 2013, sec. 1).

Conclusion

The human genetic information is differentially articulated in both time and space as discussed in the paper. These expressions, however, are finally evolving through mechanisms that we are finally beginning to understand. Moreover, substantial scientific information shows that the elongation phase is a crucial regulatory stage in cellular as well as tissue mutations. Over time studies have come to recognize, understand, and appreciate the numerous connections between cancer and problems with gene expression via transcription elongation. This realization has become particular especially to the understanding of disorders associated with the TCEBI Mutations. The identification of the potential causes of such disease especially VHL has become instrumental in the development of the necessary medication and treatment procedures. As itemized above, this paper the mainly focused on the TCEB1 gene, its associated protein, mutational variants, and potential diseases, as a result. The relationship between the gene and its components structures has also been highlighted.

References

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Appendix
RNA polymerase II general elongation factors
Data as retrieved from (SHILATIFARD, 1998, sec. 2)

The diagram above shows “Localization of the ELL2 elongation activation domain. Based on the summary of the ELL2 mutants and their activities, the transcriptional elongation activation domain of ELL2 is shown. Conserved regions 1, 2, and 3 (R1, R2, and R3) between ELL and ELL2 are indicated. The alignment of region 3 with the COOH-terminal ZO-1 binding domain of occludin.”
Diagram (b): *600788 protein 3D diagram
*600788 protein 3D diagram as retrieved from (PhosphoSitePlus, n.d.)
Diagram (c) illustrating the TCEB1 Gene in genomic location in minus strand orientation: bands according to Ensembl, locations according to Geneloc
Data information as retrieved from (GeneCards, 2014; Protein Data Bank (PDB), n.d.).
Diagram (d) showing the Schematic view of p VHL and HIF
A. Normoxia in a normal cell; HIF binds to pVHL.
B. Hypoxia in a normal cell; HIF does not bind to pVHL.
C. Cell with VHL mutation; HIF cannot bind to pVHL, therefore the cell acts as if there is constant hypoxia (information as retrieved from Frantzen, C., Links, T. P., & Giles, R. 2012).