TEDC2

Key takeaways

TEDC2 belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect TEDC2 to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of TEDC2 from memory before moving on to harder problems.

Reference excerpt

Tubulin epsilon and delta complex 2 (TEDC2), also known as Chromosome 16 open reading frame 59 (C16orf59), is a protein that in humans is encoded by the TEDC2 gene. Its NCBI accession number is NP_079384.2.

Gene

Locus TEDC2 is found on chromosome 16 at location 16p13.3, or chr16:2,460,080-2,464,963 (spanning 4883 bp) on the plus strand.

Homology and Evolution

Orthologs TEDC2 appeared between 684-797 million years ago. Its most distant ortholog is found in Branchiostoma floridae, the Florida lancelet, which diverged from other chordates around 684 million years ago. However, the gene arose more recently than 797 million years ago, when protostomes and deuterostomes diverged, as it is not found in any invertebrates. A table showing 20 selected orthologs is below, found with NCBI BLAST.

Paralogs There are no other members of the TEDC2 gene family, as it has no paralogs in any living organisms.

Expression

Transcription Factors Conserved predicted transcription factor binding sites found in the 5' region upstream of TEDC2 are WT1, ZKSCAN3 (x2), AREB6, MZF1 (x2), ATF6, ER, and P53. This suggests that these transcription factors in particular, and especially ZKSCAN3 and MZF1 on the basis of multiple conserved binding sites, are crucial in the regulation of TEDC2. ZKSCAN3 is a transcriptional repressor of autophagy, and MZF1 is thought to play a role as a tumor suppressor and regulator of cell proliferation. These conserved MZF1 sites, along with the conserved p53 site, suggest that TEDC2 could play a role in cell proliferation and can therefore impact the genesis and development of cancer.

Localization TEDC2 is predicted to be localized to the nucleus and may also be present in the cytoplasm, mitochondria, peroxisomes, and extracellular space.

Expression It is highly expressed in the testis and EBV-transformed lymphocytes. It is also highly expressed in lymph node, fetal liver, early erythroid cell, and B-lymphoblasts. It is also seen at higher levels in both embryonic stem cells and induced pluripotent stem cells than fibroblasts. Finally, relative to other genes, TEDC2 expression significantly decreases in breast cancer cells upon estrogen starvation.

Transcript Variants

The gene has 10 exons. The gene has 13 alternatively spliced transcripts, with 6 coding for a protein, 1 undergoing nonsense-mediated decay, and 6 being retained introns.

Protein

General Features TEDC2 is encoded by the TEDC2 gene with NCBI accession number NM_025108.3. The protein is 433 amino acids long with a predicted molecular weight of 46.4 kDa. There is an antibody against the protein, but a sample western blot image is not available.

Domains TEDC2 contains a domain of unknown function, DUF4693, which in humans spans from proteins 148-431, approximately the last two-thirds of the protein.

Secondary Structure Using online bioinformatics tools, TEDC2 is predicted to have many alpha helices, and it has two well-conserved predicted beta-pleated sheets near the end of the protein.

Tertiary Structure

TEDC2 is predicted to form tertiary structure based on its alpha helices. Many of these predicted alpha helices are highly conserved in orthologs, and one example of predicted tertiary structure generated by I-TASSER is shown to the right.

Post-translational Modifications

TEDC2 has a well conserved predicted O-GlcNAc site at S114 in humans. O-GlcNAcylated proteins are found mostly in the nucleus, sometimes also being found in the cytoplasm, and this is a dynamic modification, frequently being removed and reattached. TEDC2 also has three conserved, predicted C-mannosylation sites. The function of C-mannosylation is still unclear, but it is the attachment of an alpha-mannose to a tryptophan. TEDC2 also has many possible phosphorylation sites, including seven that are well-conserved. Phosphorylation is an important means of protein regulation, activation, and inactivation, so it is difficult to determine any specific function from the presence of a serine or threonine that could be phosphorylated.

Interactions

Protein-Protein Interactions KDM1A, a lysine-specific demethylase, was shown to be physically associated with TEDC2. TEDC2 also interacts with FEZ1, a fasciculation and elongation protein. FEZ1, or fasciculation and elongation protein 1, is necessary for axon growth but is also thought to be involved in transcriptional control. There is also experimental evidence for TEDC2 interaction with TUBE1 and C14orf80. TUBE1, or Tubulin epsilon 1, is involved with the centrioles during cell division, and the function of C14orf80 is unknown. TEDC2 is also co-expressed with CDC45, or cell division control protein 45, which is required for initiation of chromosomal DNA replication, as well as co-expression with CDT1, a DNA replication licensing factor required for pre-replication assembly.

Function and Clinical Significance The function of TEDC2 is not yet known with certainty by the scientific community, but its expression profile, predicted transcription factor binding sites, and other protein-protein interactions enable some predictions. TEDC2 is localized in the nucleus and is often expressed in developing tissues such as stem cells as well as differentiated fetal tissue, so it likely plays a role in DNA replication and/or cell division. This also fits with TEDC2's predicted or known protein-protein interactions, as it may interact with proteins involved in cell division (TUBE1, CDC45, CDT1), as well as remain under transcriptional control of tumor suppressors (WT1, MZF1, P53). Additionally, given the presence of an estrogen-response element binding-site, it is possible that TEDC2 plays a role in tumor development when mutated.

References

Illustrations

TEDC2: A diagram from NCBI showing TEDC2 and its gene neighborhood on chromosome 16. — A diagram from NCBI showing TEDC2 and its gene neighborhood on chromosome 16.

Worked examples

Example 1 — a first encounter with TEDC2

Start with the simplest possible case. Write down what TEDC2 claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to TEDC2 before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about TEDC2 ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of TEDC2

In research: TEDC2 appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses TEDC2 in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: TEDC2 is common in secondary-school and first-year university syllabi. It links to neighbouring topics Genes on human chromosome 16, Proteins, so understanding it makes those chapters shorter.
In everyday life: Look for TEDC2 outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

How to study TEDC2 in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what TEDC2 means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain TEDC2 out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is TEDC2 in simple terms?

Tubulin epsilon and delta complex 2 (TEDC2), also known as Chromosome 16 open reading frame 59 (C16orf59), is a protein that in humans is encoded by the TEDC2 gene. Its NCBI accession number is NP_079384.2.

Why does TEDC2 matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study TEDC2?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on TEDC2.