SOGA2

Key takeaways

SOGA2 belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect SOGA2 to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of SOGA2 from memory before moving on to harder problems.

Reference excerpt

Microtubule cross-linking factor 1, also known as Suppressor of glucose autophagy associated 2, is a protein that in humans is encoded by the MTCL1 gene (previously SOGA2, CCDC165, or KIAA0802). SOGA2 has two human paralogs, SOGA1 and SOGA3. In humans, the gene coding sequence is 151,349 base pairs long, with an mRNA of 6092 base pairs, and a protein sequence of 1586 amino acids. The SOGA2 gene is conserved in gorilla, baboon, galago, rat, mouse, cat, and more. There is distant conservation seen in organisms such as zebra finches and anoles. SOGA2 is ubiquitously expressed in humans, with especially high expression in brain (especially the cerebellum and hippocampus), colon, pituitary gland, small intestine, spinal cord, testis and fetal brain.

Gene

Locus The SOGA2 gene is located from 8717369 - 8832775 on the short arm of chromosome 18 (18p11.22).

Homology and Evolution

Paralogs There are two main paralogs to SOGA2: human protein SOGA1 and human protein SOGA3. SOGA1 has been shown to be involved in suppression of glucose by autophagy. The rate at which orthologs diverge from SOGA2 human(measured by % identity) places the approximate duplication event of SOGA1 from SOGA2 at ~254.1 MYA and the duplication event of SOGA3 from SOGA2 ~329.1 MYA.

Orthologs Many orthologs have been identified in Eukaryotes.

Distant Homologs

Homologous Domains SOGA2 is conserved farthest back in its N-terminal region, where it contains its three domains of unknown function.

Protein

Protein internal composition SOGA2 is rich in glycine (ratio r of SOGA2 composition to average human protein is 1.723), glutamate (r = 1.647), and arginine (r = 1.357). It also has a lower than usual composition of tyrosine (r = 0.3406), isoleucine (r = 0.4430), phenylalanine (r = 0.5808), and valine (r = 0.6161).

Primary structure and isoforms SOGA2 has 4 isoforms: Q9Y4B5-1, Q9Y4B5-2, Q9Y4B5-3, Q9Y4B5-4.

Domains and motifs SOGA2 contains Domain of Unknown Function 4201 (DUF4201) from aa 16-235. This domain is specific to the Coiled Coil Domain Containing family of proteins in eukaryotes. It also contains two copies of Domain of Unknown Function 3166 (DUF3166): one from aa 140-235 and one from aa 269-364.

Post-translational modifications SOGA2 is expected to undergo a number of post-translational modifications. Modifications of human SOGA2 that are shared by orthologs include:

Sumoylation at amino acids 87, 152, 235, 392, and 1379. Sulfination at tyrosines 14 and 1249. Phosphorylation at a number of sites, highlighted in the following graphic:

Secondary structure The consensus of the prediction software PELE, GOR4, and SOSUICoil is that the secondary structure of SOGA2 is dominated by alpha helices with interspersed regions of random coil. GOR4 indicated that SOGA2 is dominated by alpha-helices; it predicted a mere 5.61% of residues in an extended strand (parallel or antiparallel Beta-sheet) conformation, as opposed to 47.79% alpha helix and 46.6% random coils.

Tertiary structure SOGA2 shares sequence features in its highly conserved N-terminal region. This homology allows prediction of its tertiary structure on the basis of homology to published 3d structures via Phyre2 and NCBI structure.

Gene expression

Promoter The promoter for human SOGA2 is below.

Gene expression data The EST profile shows that, in humans, SOGA2 is highly expressed in many sites throughout the body, including bone, brain, ear, eye, and many others. There are a large number of transcripts in liver cancer samples. Human microarray data show that SOGA2 is moderately expressed, with especially high expression in brain (especially the cerebellum and hippocampus), colon, pituitary gland, small intestine, spinal cord, testis and fetal brain. Brain-tissue-specific microarray data show that SOGA2 has high expression throughout the posterior lobe of the cerebellar hemispheres and posterial lobe of the vermis in the mouse brain. There is low expression in most other areas of the brain.

Transcript variants In humans, the SOGA2 gene produces 17 different transcripts, 8 of which form a protein product (one undergoes nonsense mediated decay). The main transcript in humans is transcript ID ENST00000359865, or SOGA2-001.

Function

Possible transcription factors Possible transcription factors for human SOGA2 include:

Modulator recognition factor 2 cAMP-responsive element binding protein 1 alternative splicing variant of FOXP1 MDS1/EVI1-like gene 1 Ikaros 2, possible regulator of lymphocyte differentiation

Interactions Protein complex co-immunoprecipitation (Co-IP) experiments revealed interacting proteins such as cell death regulators, ATP-binding cassette (ABC) transporters and protein kinase A binding proteins. The 540 interacting proteins include ABCF1, ACTB, ACTL6A, BCLAF1, BCLAF1, CHEK1, and MAGEE2. K-nearest neighbor analysis by wolf pSort indicates that in humans, SOGA2 is focused mainly in the nucleus, cytoplasm, and the cytonuclear space. There is a small chance that it is localizes to the golgi. A number of protein interactants were also identified via the STRING database, including MARK2, MARK4, and PPP2R2B.

Clinical significance SOGA2 has no currently known disease associations or mutations.

References

Illustrations

Worked examples

Example 1 — a first encounter with SOGA2

Start with the simplest possible case. Write down what SOGA2 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 SOGA2 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 SOGA2 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 SOGA2

In research: SOGA2 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 SOGA2 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: SOGA2 is common in secondary-school and first-year university syllabi. It links to neighbouring topics Cell cycle regulators, Genes on human chromosome 18, so understanding it makes those chapters shorter.
In everyday life: Look for SOGA2 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 SOGA2 in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what SOGA2 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 SOGA2 out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is SOGA2 in simple terms?

Microtubule cross-linking factor 1, also known as Suppressor of glucose autophagy associated 2, is a protein that in humans is encoded by the MTCL1 gene (previously SOGA2, CCDC165, or KIAA0802). SOGA2 has two human paralogs, SOGA1 and SOGA3.

Why does SOGA2 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 SOGA2?

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 SOGA2.