Research
I am a microbiologist and I study the viruses that infect bacteria (bacteriophages).
During my PhD in the Bondy-Denomy lab at UCSF, I studied how bacteriophages use anti-CRISPR proteins to survive being attacked by the bacterial CRISPR-Cas immune system. As a Miller Research Fellow in Jill Banfield's lab, I used genome-resolved metagenomics to discover phages that use alternative genetic codes in human and animal microbiomes.
As a Scientist at Arcadia Science, I combine experimental and metagenomic techniques to explore the amazing diversity of bacteriophages on our planet.
Education
PhD in Biomedical Sciences 2014-2020
Advisor: Joe Bondy-Denomy
University of California, San Francisco
BSc in Microbiology 2010-2014
Advisor: Jon Boyle
University of Pittsburgh
Publications
2022
Peters
S, Borges AL, Giannone RJ, Morowitz M, Banfield JF, Hettich R. Validation that human microbiome phages use
alternative genetic coding with TAG stop read as Q. bioRxiv.
(2022). doi: https://doi.org/10.1101/2022.01.06.475225
2021
Rubin
BE, Diamond S, Cress BF, Crits-Christoph A, Lou YC, Borges AL, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Rovinksy R, Smock
DCJ, Tang K, Owend TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM,
Banfield JF, Doudna JA. Species- and site-specific
genome editing in complex bacterial communities. Nat. Microbiol. (2021).
Chen LX, Jaffe AL, Borges AL, Penav PI, Nelson TC, Warren LA, Banfield JF. Phage-encoded ribosomal protein S21 expression is linked to late stage phage replication. bioRxiv. (2021). doi: https://doi.org/10.1101/2021.10.11.463225
Borges AL, Lou YC, Sachdeva R, Al-Shayeb B, Jaffe AL, Santini JM, Banfield JF. Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes. bioRxiv. (2021). doi: https://doi.org/10.1101/2021.08.26.457843
Crisci MA, Chen LX, Devoto AE, Borges AL , Bordin N, Sachedeva R, Tett A, Sharrar AM, Segata N, Debenedetti F, Burt R, Wood RM, Rowden LJ, Corsini PM, van Winden S, Holmes MA, Lei S, Banfield JF, Santini JM. Closely related Lak megaphages replicate in the microbiomes of diverse animals. iScience : 102875 (2021).
Borges AL. How to train your bacteriophage. [Commentary] PNAS 118 (28) (2021).
Borges AL. The Art of
Being Single. [Commentary] The CRISPR Journal 4(1):16-17 (2021).
Leon LM, Park AE, Borges AL, Zhang JY, Bondy-Denomy J. Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa. Nucleic Acids Res. (2021). doi:10.1093/nar/gkab006
2020
Gussow AB, Park AE, Borges AL, Shmakov SA, Makanrova KS, Wolf YI, Bondy-Denomy J, Koonin EV. Novel anti-CRISPR protein families predicted with a machine-learning approach. Nat. Comms. 11(1): 3784. (2020).
Govindarajan S, Borges AL, Bondy-Denomy J. Distinct subcellular localization of a Type I CRISPR complex and the Cas3 nuclease in bacteria. bioRxiv (2020). doi: https://doi.org/10.1101/2020.09.29.318501
Borges AL, Castro B, Govindarajan S, Solvik T, Escalante V, Bondy-Denomy J. Bacterial alginate regulators and phage homologs repress CRISPR-Cas immunity. Nat. Microbiol. 5(5): 679-687.(2020).
- Behind the paper: Transcription Factors for Hire.
2019
Crowley VM, Catching A, Taylor HN, Borges AL, Metcalf J, Bondy-Denomy J, Jackson R.A. A Type IV-A CRISPR-Cas system in Pseudomonas aeruginosa mediates RNA-guided plasmid interference in vivo. The CRISPR Journal 2(6):434-440. (2019).
Stanley SY, Borges AL, Chen K, Swaney DL, Krogan NJ, Bondy-Denomy J, Davidson AR. Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription. Cell 178(6):1452-1464 (2019).
Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes. Nat Microbiol. 4(11):1894-1906 (2019).
2018
Marino ND*, Zhang JY*, Borges AL*, Sousa AA, Leon LM, Rauch BJ, Walton RT, Berry JD, Joung JK, Kleinstiver BP, Bondy-Denomy J. Discovery of widespread Type I and Type V CRISPR-Cas inhibitors. Science 362(6411):240-242 (2018).
* These authors contributed equally to this work
- Koonin E, Makarova K. Anti-CRISPRs on the March. Science. 2018
Borges AL, Zhang JY, Rollins MF, Osuna BA, Wiedenheft B, Bondy-Denomy J.Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity. Cell 174(4):917-925 (2018).
- Bernheim A, Sorek R. Viruses cooperate to defeat bacteria. Nature News and Views. 2018
- Nussenzweig PM, Marraffini LA. Viral Teamwork Pushes CRISPR to the Breaking Point. Cell. 2018
- van Gent M, Gack MU. Viral Anti-CRISPR Tactics: No Success without Sacrifice. Immunity. 2018
2017 and prior
Borges AL, Davidson AR, Bondy-Denomy J. The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs. Annu. Rev. Virol. 4(1):37-59 (2017).
Walzer KA, Wier GM, Dam RA, Srinivasan AR, Borges AL, English ED, Herrmann DC, Schares G, Dubey JP and Boyle JP. Hammondia hammondi harbors functional orthologs of the host-modulating effectors GRA15 and ROP16 but is distinguished from Toxoplasma gondii by a unique transcriptional profile. Eukaryot. Cell 13(12):1507-18 (2014).
Adomako-Ankomah Y, Wier GM, Borges AL, Wand HE and Boyle JP. Differential locus expansion distinguishes Toxoplasmatinae species and closely related strains of Toxoplasma gondii. MBio 5(1):e01003-13 (2014).