Microbial sequence databases contain a wealth of knowledge about enzymes and other molecules that could possibly be adapted for biotechnology. But these databases have grown so large in recent times that they’ve change into difficult to go looking efficiently for enzymes of interest.
Now, scientists on the McGovern Institute for Brain Research at MIT, the Broad Institute of MIT and Harvard, and the National Center for Biotechnology Information (NCBI) on the National Institutes of Health have developed a latest search algorithm that has identified 188 kinds of recent rare CRISPR systems in bacterial genomes, encompassing hundreds of individual systems. The work appears today in .
The algorithm, which comes from the lab of pioneering CRISPR researcher Professor Feng Zhang, uses big-data clustering approaches to rapidly search massive amounts of genomic data. The team used their algorithm, called Fast Locality-Sensitive Hashing-based clustering (FLSHclust) to mine three major public databases that contain data from a wide selection of surprising bacteria, including ones present in coal mines, breweries, Antarctic lakes, and dog saliva. The scientists found a surprising number and variety of CRISPR systems, including ones that would make edits to DNA in human cells, others that may goal RNA, and plenty of with a wide range of other functions.
The brand new systems could potentially be harnessed to edit mammalian cells with fewer off-target effects than current Cas9 systems. They might also sooner or later be used as diagnostics or function molecular records of activity inside cells.
The researchers say their search highlights an unprecedented level of diversity and adaptability of CRISPR and that there are likely many more rare systems yet to be discovered as databases proceed to grow.
“Biodiversity is such a treasure trove, and as we proceed to sequence more genomes and metagenomic samples, there may be a growing need for higher tools, like FLSHclust, to go looking that sequence space to seek out the molecular gems,” says Zhang, a co-senior creator on the study and the James and Patricia Poitras Professor of Neuroscience at MIT with joint appointments within the departments of Brain and Cognitive Sciences and Biological Engineering. Zhang can also be an investigator on the McGovern Institute for Brain Research at MIT, a core institute member on the Broad, and an investigator on the Howard Hughes Medical Institute. Eugene Koonin, a distinguished investigator on the NCBI, is co-senior creator on the study as well.
Looking for CRISPR
CRISPR, which stands for clustered frequently interspaced short palindromic repeats, is a bacterial defense system that has been engineered into many tools for genome editing and diagnostics.
To mine databases of protein and nucleic acid sequences for novel CRISPR systems, the researchers developed an algorithm based on an approach borrowed from the massive data community. This system, called locality-sensitive hashing, clusters together objects which might be similar but not exactly equivalent. Using this approach allowed the team to probe billions of protein and DNA sequences — from the NCBI, its Whole Genome Shotgun database, and the Joint Genome Institute — in weeks, whereas previous methods that search for equivalent objects would have taken months. They designed their algorithm to search for genes related to CRISPR.
“This latest algorithm allows us to parse through data in a time-frame that’s short enough that we are able to actually get well results and make biological hypotheses,” says Soumya Kannan PhD ’23, who’s a co-first creator on the study. Kannan was a graduate student in Zhang’s lab when the study began and is currently a postdoc and Junior Fellow at Harvard University. Han Altae-Tran PhD ’23, a graduate student in Zhang’s lab throughout the study and currently a postdoc on the University of Washington, was the study’s other co-first creator.
“This can be a testament to what you’ll be able to do whenever you improve on the methods for exploration and use as much data as possible,” says Altae-Tran. “It’s really exciting to have the ability to enhance the dimensions at which we search.”
Recent systems
Of their evaluation, Altae-Tran, Kannan, and their colleagues noticed that the hundreds of CRISPR systems they found fell into just a few existing and plenty of latest categories. They studied several of the brand new systems in greater detail within the lab.
They found several latest variants of known Type I CRISPR systems, which use a guide RNA that’s 32 base pairs long somewhat than the 20-nucleotide guide of Cas9. Due to their longer guide RNAs, these Type I systems could potentially be used to develop more precise gene-editing technology that’s less vulnerable to off-target editing. Zhang’s team showed that two of those systems could make short edits within the DNA of human cells. And since these Type I systems are similar in size to CRISPR-Cas9, they might likely be delivered to cells in animals or humans using the identical gene-delivery technologies getting used today for CRISPR.
One among the Type I systems also showed “collateral activity” — broad degradation of nucleic acids after the CRISPR protein binds its goal. Scientists have used similar systems to make infectious disease diagnostics corresponding to SHERLOCK, a tool able to rapidly sensing a single molecule of DNA or RNA. Zhang’s team thinks the brand new systems could possibly be adapted for diagnostic technologies as well.
The researchers also uncovered latest mechanisms of motion for some Type IV CRISPR systems, and a Type VII system that precisely targets RNA, which could potentially be utilized in RNA editing. Other systems could potentially be used as recording tools — a molecular document of when a gene was expressed — or as sensors of specific activity in a living cell.
Mining data
The scientists say their algorithm could aid within the seek for other biochemical systems. “This search algorithm could possibly be utilized by anyone who desires to work with these large databases for studying how proteins evolve or discovering latest genes,” Altae-Tran says.
The researchers add that their findings illustrate not only how diverse CRISPR systems are, but additionally that almost all are rare and only present in unusual bacteria. “A few of these microbial systems were exclusively present in water from coal mines,” Kannan says. “If someone hadn’t been interested by that, we may never have seen those systems. Broadening our sampling diversity is admittedly vital to proceed expanding the range of what we are able to discover.”
This work was supported by the Howard Hughes Medical Institute; the K. Lisa Yang and Hock E. Tan Molecular Therapeutics Center at MIT; Broad Institute Programmable Therapeutics Gift Donors; The Pershing Square Foundation, William Ackman and Neri Oxman; James and Patricia Poitras; BT Charitable Foundation; Asness Family Foundation; Kenneth C. Griffin; the Phillips family; David Cheng; and Robert Metcalfe.
