The CRISPR Codex: Decoding Gene Editing with Syed Muiz

Chapter 1 of The CRISPR Codex:

CRISPR-Cas Technology – A Simplified Guide

by Syed Muiz for BioVerse

 

Welcome to The CRISPR Codex – a science series focused on the powerful gene editing tool called CRISPR. In this first part, I'll make the foundation by talking about how CRISPR was discovered and how it works  and how it’s being used in real-life genetic engineering.

CRISPR-Cas systems are a built-in immune system found in bacteria and other simple organisms. It is highly diverse adaptive & specific (I'll explain this later in this series) microbial immune system used by most archaea (~90%) and many eubacteria (~40%) to protect thmselves from invading viruses and plasmids. At first it found as a strange DNA pattern in E. coli bacteria back in the 1980s and its now become one of the most powerful tools in genetic engineering. These system allow the cell to recognize and distinguish incoming 'foreign' DNA from 'self' DNA. CRISPR-Cas system consist of two general parts: CRISPRs (Clustered Regularly Inter-spaced Short Palindromic Repeats) and Cas (CRISPR-associated) protein. CRISPER-Cas consist highly conserved short repeated sequences separated by similarly sized short spacers sequences and they are unique sequences originating from viral or plasmid DNA. A spacer works like a memory cell in our immune system or like how a vaccine trains our body, it stores a viral DNA sample so the bacteria can recognize and fight that same virus in the future. By adding new spacers in their genome, bacteria able to recognize new matching viral DNA or plasmid genomes. The size of CRISPR repeats and spacers varies between 23 to 47 bp and 21 to 72 bp, respectively. The bacterial genome contain more then one locus and they are highly diverse and hypervariable spacer sequences, even between closely related strains. 

Another feature associated with CRISPR loci is the presence of a conserved sequence, called the Leader. It sits just upstream of the CRISPR array, in the direction where transcription begins. This Leader sequence acts like a starting signal, helping in the proper transcription of CRISPR RNAs (crRNAs). It also plays a role in guiding the integration of new spacers, making sure they're always added to the same end, like how new files always go on top in a stack. CRISPER activity requires a set of CRISPR-associated (cas) genes, which are usually found closely to the CRISPER and that code for cas protein essential to the immune response. These cas proteins perform a variety of functions, including DNA cleavage, RNA processing, and interacting with other CRISPR components. Different types of cas proteins, like Cas9, Cas12, and others, are used for specific tasks within the CRISPR system. In CRISPR-Cas systems currently being grouped into two classes, six types, and over 30 subtypes.

 CRISPR-Cas system types:

🔹Class 1: Multi-Protein Effector Complexes

Type I (Signature protein: Cas3)

• Subtypes: I-A, I-B, I-C, I-D, I-E, I-F1, I-F2, I-F3, I-G​MDPI

Type III (Signature protein: Cas10)

• Subtypes: III-A, III-B, III-C, III-D, III-E, III-F​

Type IV (Signature proteins: Cas5, Cas7, Cas8-like)

• Subtypes: IV-A, IV-B, IV-C​

 🔹 Class 2: Single-Protein Effector Modules

Type II (Signature protein: Cas9)

• Subtypes: II-A, II-B, II-C​

Type V (Signature protein: Cas12)

• Subtypes: V-A, V-B, V-C, V-D, V-E, V-F1, V-F2, V-F3, V-G, V-H, V-I, V-J, V-K, V-U1, V-U2, V-U3, V-U4, V-U5​

Type VI (Signature protein: Cas13)

• Subtypes: VI-A, VI-B1, VI-B2, VI-C, VI-D​

So this was just an intro part that builds a base for understanding the CRISPR-Cas technique. In the next chapter, I’ll talk about the general working mechanism of this system — how it actually detects, targets, and cuts the foreign DNA. That part will clear how this microbial immune system works step by step. 🔗Chapter 2🔗