Question

In the publication that provided the first evidence of CRISPRCas as an adaptive immune system [Barrangou, R., et al. (2007). Science. \(315: 1709-1712\) ], the authors state that CRISPR-Cas "provides a historical perspective of phage exposure, as well as a predictive tool for phage sensitivity." Explain how this is true using what you know about the CRISPR locus.

Short answer

Based on the provided solution, explain how the CRISPR-Cas system serves as a historical perspective of phage exposure and a predictive tool for phage sensitivity. The CRISPR-Cas system serves as a historical perspective of phage exposure by storing spacer sequences derived from phage DNA within the CRISPR locus. These spacer sequences represent "archives" of past viral infections in the bacterial genome. As a bacteria encounters and survives phage attacks, more spacer sequences accumulate in the CRISPR locus, creating a historical record of phage exposure. Additionally, the CRISPR-Cas system functions as a predictive tool for phage sensitivity by providing information about the bacteria's immunity against specific phages. Examining the spacer sequences within the CRISPR locus allows researchers to determine which phages the bacteria have developed immunity against, thereby predicting their sensitivity to particular viral infections.

Step-by-step solution

Understanding CRISPR-Cas system

The CRISPR-Cas system is a prokaryotic adaptive immune system that provides resistance to foreign genetic elements like phages (viruses that infect bacteria). This system contains a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) locus which is a set of repeated sequences in bacterial DNA, separated by spacer sequences derived from phage DNA. The loci consist of a combination of memory and recognition elements that facilitate identifying and neutralizing viral infections.

Historical perspective of phage exposure

The CRISPR locus holds the "archives" of past viral infections in the form of spacer sequences. Each time a bacteria survives a phage attack, a small portion of the phage's DNA is integrated into the bacterial genome as a new spacer, sandwiched between two repeat sequences. As more phage infections are encountered and survived, the CRISPR locus accumulates more spacer sequences, creating a historical record of phage exposure within the bacterial genome.

Adaptive immunity

When a bacteria with a CRISPR-Cas system encounters a phage it has previously encountered, the spacer sequences act as a "genetic memory" of past infections. The CRISPR locus is transcribed into RNA (called crRNA), which targets and binds to the corresponding, matching phage sequence in invading genetic elements. This crRNA then guides the Cas (CRISPR-associated) proteins to cleave the targeted phage DNA, preventing the phage from propagating and providing adaptive immunity against the phage.

Predictive tool for phage sensitivity

By examining the spacer sequences within a bacterial CRISPR locus, researchers can determine which phages the bacteria have been previously exposed to and potentially which phages it has developed immunity against. The presence or absence of specific spacer sequences serves as a predictive tool for determining the phage sensitivity of a bacterial strain. In conclusion, the CRISPR locus in prokaryotes provides a historical perspective of phage exposure by storing spacer sequences from previously encountered phages. It also serves as a predictive tool for phage sensitivity since the presence of specific spacer sequences indicates immunity against those specific phages.

Key concepts

Adaptive Immunity

Adaptive immunity in the CRISPR-Cas system is the process by which bacteria and archaea build a defense against viruses, specifically bacteriophages. Unlike innate immunity, which is pre-existing, adaptive immunity develops as the organism is exposed to new pathogens.
In prokaryotes, this immunity works through the integration of short sequences of DNA, called spacers, from invaders like bacteriophages into their own genome at the CRISPR locus. The bacteria use this genetic memory to recognize and combat future infections by the same or similar phages.

• Steps: Bacterial cells are infected by a phage.
• Small fragments of the phage DNA are captured by the CRISPR proteins.
• These DNA fragments are then inserted as spacer sequences in the CRISPR array.

The next time the phage attacks, the bacterium expresses RNA molecules from the CRISPR-spacer sequences that guide Cas proteins to the phage DNA, enabling precise targeting and destruction. This targeted mechanism is highly specific due to its reliance on the memory stored in the spacer sequences, providing a fascinating and effective form of adaptive immunity.

Phage Sensitivity

Phage sensitivity refers to the susceptibility of bacteria to infection by specific bacteriophages. The CRISPR-Cas system plays a key role in modulating this sensitivity.
By analyzing the CRISPR spacer sequences in the bacterial genome, scientists can identify which viruses have previously attacked the bacteria. These sequences act like a "mug shot" collection of past viral invaders.
Bacteria with CRISPR spacers corresponding to a specific phage are likely immune to it, thereby displaying reduced sensitivity. Conversely, if the bacterium lacks a particular spacer against a new phage, it remains sensitive to that phage's attack.
Phage sensitivity is crucial in studies of bacterial-phage interactions and has applications in phage therapy, where phages are used to target pathogenic bacteria without affecting beneficial microbes. The ability to predict phage sensitivity through CRISPR analysis is therefore a powerful tool in both environmental microbiology and medical research.

Spacer Sequences

Spacer sequences are short segments of DNA incorporated into the bacterial genome between the repetitive CRISPR sequences.
These sequences are derived from the DNA of bacteriophages and other foreign genetic elements that have previously attacked the bacterium.
Spacer sequences essentially serve as a genetic archive, maintaining a record of past infections. Each spacer represents a "memory" of a specific viral encounter, allowing the bacteria to recognize and fight off repeat infections by the same virus.
When a phage attacks a bacterium, the CRISPR system selects a portion of the phage's DNA to incorporate into the CRISPR locus as a new spacer. As time goes on, this CRISPR array builds up a library of spacers, enhancing the bacterium’s ability to respond quickly to previously encountered phages.
The process of spacers encoding and archiving information is dynamic, allowing bacteria to adapt and enhance their immune capabilities over generational time.

Prokaryotic Immune System

The prokaryotic immune system, as exemplified by the CRISPR-Cas system, is an extraordinary mechanism that protects bacteria and archaea against foreign DNA.
It functions similarly to the immune systems found in more complex organisms, despite its unique approach. This system not only defends against invaders like viruses but also learns from these encounters.
Unlike in eukaryotic organisms, where immunity largely involves complex cellular responses, prokaryotic immunity via CRISPR is based on direct DNA recognition and cleavage.

• The CRISPR array captures "genetic snapshots" from invaders to prevent future attacks.
• Integrated spacers act as molecular guides for the Cas proteins to locate and destroy invading phage DNA upon re-infection.

This memory-based component makes the prokaryotic immune system adaptive, providing a specific defense strategy that can be tailored over time through the accumulation of spacer sequences. This ongoing process showcases the evolutionary ingenuity of microbial organisms in surviving hostile environments.