Studying Autophagy in Flies Using CRISPR


Transcribed RNA can be used to study RNA structure and how it relates to function or how proteins and RNA interact. It can also be used for gene silencing using RNAi (studied more often as a possible therapeutic option) or simply serve as a molecular standard in Real-time RT-PCR. Transcribed RNA is also used in Class 2 Clustered Regularly Interspaced Short Palindromic Repeat systems, or CRISPR.

The CRISPR system, which is naturally occurring in bacteria, has been manipulated to perform gene editing in a laboratory environment. To perform CRISPR in the laboratory environment, you need two main reagents:

  1. The Brains: Guide RNA (gRNA or sgRNA) – Small piece of RNA containing a nucleotide sequence that is capable of binding the chosen Cas Protein, and contains a portion of the sequence that can bind the DNA the researcher intends to modify – the target DNA.
  2. The Brawn: CRISPR-associated endonuclease (Cas Protein) – The protein that cleaves the target DNA; the most popular Cas protein is called Cas9. The Cas protein is guided by the (gRNA).

Recently, Guo et al. used Promega’s RiboMAX™ Large-Scale RNA Production System to produce gRNA to be used in CRISPR for their study to determine the effects of the loss of, or mutations in, a specific gene in fruit flies (1).  Atg101 is a gene that plays an important role in autophagy, an intracellular pathway for removing toxins or damaged parts of cells. Continue reading “Studying Autophagy in Flies Using CRISPR”

How Autophagy Feeds Cancer’s Need for Metabolites

Illustration of energy metablism in cell.Metabolism underpins numerous cellular processes. Without it, cells would not grow, divide, synthesize or secrete. Another pathway, autophagy, degrades unwanted cellular materials, helping to maintain cell health. With these opposing roles, is there a connection between autophagy and metabolism? As it turns out, the answer is yes. Because molecules degraded by autophagy are recycled and fed into metabolism pathways as precursor compounds. There are interesting implications as a result of this connection, ones that affect cancer cells as described in a recent Cell Metabolism review article.

Autophagic flux, the process by which molecules and organelles are directed to the autophagosome, fuse with the lysosome and are degraded, involves a selective process that determines the cargo carried within the autophagosome. Autophagy-related genes (ATGs) direct the process and particular receptor proteins bind the cargo. What is interesting about the connection among cancer, autophagy and metabolism is the complexity of the role that autophagy plays in cancer. While autophagy was thought to act in a more tumor suppressive manner as shown when one copy of an ATG6 analogous gene in mice was deleted and the other left unaltered, and malignant tumors developed, but in mice mosaic for ATG5 deletions, the inhibition of autophagy resulted in benign tumors in the liver. This latter experiment suggested autophagy was needed for cancer progression, a hypothesis reinforced by the lack of ATG mutations in human cancers. Continue reading “How Autophagy Feeds Cancer’s Need for Metabolites”

Autophagy: The Intersection of Vitamin D, HIV and Tuberculosis

HIV-1 particles assembling at the surface of an infected macrophage. By see Source [CC-BY-2.5 (], via Wikimedia Commons
With the warmer season in full swing in Wisconsin, the grass needs mowing and the weeds need pulling. As a consequence, I am outside in the sun, synthesizing Vitamin D (and watching my freckles multiply). The benefits of this vitamin have been discussed in the news (e.g., may help prevent cancer, maintains a healthy working brain) while informing us most people lack adequate levels. A recent PLoS Pathogens article intrigued me because the researchers examined the role Vitamin D played in mitigating human immunodeficiency virus type-1 (HIV) and Mycobacterium tuberculosis coinfection in macrophages.

Why were Campbell and Spector interested in Vitamin D’s effect on HIV-1 and M. tuberculosis? Continue reading “Autophagy: The Intersection of Vitamin D, HIV and Tuberculosis”