CTY Family Day 2013

Carnegie Institution for Science
Department of Embryology

Recent technological advancements have led to an explosion in the amount of information available about the genes and proteins present in organisms ranging from viruses to bacteria to plants to humans. In this workshop, you will be introduced to some of the publicly accessible tools and genomic databases that allow anyone with an internet connection to explore how genes in fundamental biological processes are conserved between model organisms and man.




 

Night and Day: Regulating circadian rhythm with cryptochromes

Many organisms vary their activities according to the time of day. These circadian (circa- "approximately" -dian "a day") rhythms help find prey and avoid predators. A protein called cryptochrome acts to coordinate circadian rhythms with changes in the daily sunrise and sunset.

  • Obtain the protein sequence for the fruitfly cryptochrome gene (cry) from FlyBase
  • Compare the sequence of fruitfly and human homologs using protein blast
  • Compare structure of fruitfly (4GU5) and mammalian (4I6E) proteins at PDB
  • BONUS: Determine where human cryptochrome (cry2) is expressed using BioGPS

 

A Tight Squeeze: Packing 2 meters of DNA into each cell with histones

It's no small feat to package DNA into a cell! If the DNA from a single human cell were fully stretched out, it would reach 2 meters in length. To fit inside a volume smaller than you can see with your naked eye, the highly negatively charged DNA is spooled around highly positively charged proteins called histones. When you look at chromosomes, you are actually looking at DNA that is tightly wound in protein. In this example, you will compare the combined structure of DNA and histones in frogs versus humans.

  • Obtain the protein sequence for the frog histone 4 gene (hist1h4) from XenBase
  • Compare the sequence of frog and human homologs using protein blast
  • Compare structure of frog (3UT9) and human (3W96) proteins at PDB
  • BONUS: Determine where human histone (hist1h2bj) is expressed using BioGPS

 

Muscle or Blood: Determining cell fate with transcription factors

How cells become one type rather than another (e.g. muscle vs blood) is determined in part by proteins called transcription factors. The MyoD transcription factor helps make muscle cells by decoding information stored in DNA using a helix-loop-helix domain. Variations of this domain have been adapted for use in other transcription factors over evolution to make other cell types. In this example, you will compare the helix-loop-helix domain bound to DNA in the MyoD and LMO2 transcription factors.

  • Obtain the protein sequence for the mouse MyoD gene (myod1) from MGI
  • Compare the sequence of mouse and human homologs using protein blast
  • Compare structure of the helix-loop-helix domain in mouse MyoD (1MDY) and human LMO2 (2YPA) proteins at PDB
  • BONUS: Determine where human (lmo2) is expressed using BioGPS

 
 

Under Water: Transporting oxygen in blood with hemoglobin

Almost all living organisms need oxygen. Hemoglobin is the protein that transports oxygen in human blood (red blood cells) from lungs to the tissues of the body. A single Hemoglobin can carry four molecules of oxygen! In this example, you will compare the structure of fish and human hemoglobin proteins, and get an appreciation of how similar or different these essential proteins are in different organisms.

  • Obtain the protein sequence for the zebrafish adult hemoglobin gene (hbaa1) from ZFIN
  • Compare the sequence of zebrafish and human homologs using protein blast
  • Compare structure of fish (1OUU) and human (1HHO) proteins at PDB
  • BONUS: Determine where human hemoglobin (hba1) is expressed using BioGPS

 
 

The Sweet Life: Metabolising sugar with glucosidases

Sugar is essential for many processes: storage and source of energy or even signaling within a cell! To go from storage to use, the cell needs to break down large complexes of sugar molecules into basic building blocks. Proteins like rice beta-glucosidase help regulating these processes essential in EVERY organism. In this example, we will compare beta-glucosidase of rice versus human.

  • Obtain the protein sequence for the rice beta-glucosidase 6 gene (bglu6) from UniProt
  • Compare the sequence of rice and human homologs using protein blast
  • Compare structure of rice (3GNO) and human (3VKK) proteins at PDB
  • BONUS: Determine where human glucosidase (gba3) is expressed using BioGPS

 

A Xerox Copier: Ensuring proper genome duplication with PCNA

DNA contains the genetic code that provides a cell its identity. To propagate their identity, cells duplicate their DNA content prior to division into 2 identical daughter cells. The super compacted DNA opens up and a sliding clamp encircles DNA that is central to DNA replication to form an accesible platform for the copying machinery. PCNA is such a sliding clamp.

  • Obtain the protein sequence for the mustard plant gene (ATPCNA1) from TAIR
  • Compare the sequence of plant and human homologs using protein blast
  • Compare structure of plant (2ZVV) and human (1W60) proteins at PDB
  • BONUS: Determine where human (PCNA) is expressed using BioGPS

 

[BONUS] Antifreeze Proteins: A Case of Convergent Evolution

Convergent evolution occurs when different species use different proteins to independently evolve the same function (much like evolution of the wing, where flying birds, insects and bats have developed the capacity to fly independently.) By evolving Antifreeze proteins, which inhibit the growth of ice crystals, some fish and animals have independently evolved an incredible capacity to stay alive at freezing temperatures! In this example, you will compare the structure of fish and beetle Antifreeze Proteins, and learn if humans and other organisms have them.

  • Obtain the protein sequence for the winter flounder antifreeze gene (hplc6) from UniProt
  • See if any other organisms have a similar protein using protein blast
  • Compare structure of antifreeze proteins from the winter flounder (1WFB) and mealworm beetle (1EZG) proteins at PDB

Special thanks to Valeriya Gaysinskaya, Pavol Genzor, Safia Malki, Zehra Nizami, and Gaëlle Talhouarne for devising these examples