Selective maintenance of multiple CRISPR arrays across prokaryotes

Abstract

Prokaryotes are under nearly constant attack by viral pathogens. To protect against this threat of infection, bacteria and archaea have evolved a wide array of defense mechanisms, singly and in combination. While immune diversity in a single organism likely reduces the chance of pathogen evolutionary escape, it remains puzzling why many prokaryotes also have multiple, seemingly redundant, copies of the same type of immune system. Here, we focus on the highly flexible CRISPR adaptive immune system, which is present in multiple copies in a surprising 21% of the prokaryotic genomes in RefSeq. We use a comparative genomics approach looking across all prokaryotes to demonstrate that having more than one CRISPR system confers a selective advantage to the organism, on average. We hypothesize that a tradeoff between memory span and learning speed could select for both "long-term memory" and "short-term memory" CRISPR arrays, and we go on to develop a mathematical model to confirm that such a tradeoff could lead to selection for multiple arrays.

The size of the immune repertoire of bacteria

“…8 assumed an exponential decay in expression of leader-distant spacers; both found that a repertoire of five to seven spacers is sufficient to optimize immunity. However, actual CRISPR repertoires consist of many more spacers (2, 7-9) distributed across multiple cassettes (5), with many dozens of spacers translated into RNA in a sporadic manner across each cassette despite a gradual decay in expression from the leader end (12)(13)(14). Thus, we pursued the alternative hypothesis that the primary role of CRISPR is to retain a long-term memory of previous invasions to guard against the diverse landscape of phage species (15).…”

“…The CRISPR-Cas mechanism for immunity has three stages (2,3). Following a first encounter with a virus, after a successful defense through another mechanism or if the virus is ineffective for some reason (4), some of the Cas proteins recruit pieces of viral DNA and integrate these spacers into an array separated by palindromic repeated sequences in one of several CRISPR loci (5) of the bacterial genome. Each array defines a CRISPR cassette, and together, the cassettes carry a memory of past infections.…”

“…There is a general decline in expression level of spacers with distance from the leader end of an array, but while promoter-proximal spacers are preferentially expressed, the decline away from the leader end is gradual, the expression pattern is sporadic, there can be internal promoters leading to enhanced expression of distal spacers, and sometimes there is even additional transcription in the reverse sense. Taking these patterns and the report of the common presence of multiple CRISPR arrays in a single genome (5) into account, typical prokaryotes enjoying CRISPR-based immunity show significant expression of a few dozen to a few hundred spacers.…”

“…Because of finding 3, given a cost for having more spacers either in fitness or due to the specific mechanisms of CRISPR-based immunity, prokaryotes should only carry about a half-dozen spacers (8,16). Since typical prokaryotes express a few dozen to a few hundred spacers (5,(12)(13)(14), we need an alternative theoretical explanation for the size of CRISPR arrays.…”

How important is CRISPR-Cas for protecting natural populations of bacteria against infections by mobile genetic elements?

“…Finally, our understanding of the ecological and evolutionary consequences of CRISPR-Cas immune responses are limited to in vitro experiments that lack much of the biotic and abiotic complexity of natural environments. Could it be that the biotic and abiotic complexity of the real world, where communities of microbes include multiple species and strains as well as diversity in phage and plasmids, are spatially structured and exist in fluctuating environments are critical to the evolution and maintenance of CRISPR (50,85,139,140)? Filling these gaps in our current understanding of CRISPR ecology and evolution requires interdisciplinary approaches that combine observational studies, mathematical and computer simulation models, as well as population and evolutionary dynamics experiments.…”