Trimming the unknowns: identifying the function of primate TRIM34

From the Ohainle and Emerman labs, Human Biology and Basic Sciences Divisions

When you hear the words ‘restriction’ and ‘virus,’ you might think of pandemic-related travel and social constraints to curb viral transmission. However, there’s also restriction against viruses that plays out on the molecular level.

Restriction factors are host antiviral proteins that inhibit, or restrict, viral replication and transmission, often by recognizing and binding to the viral capsid. Many primate restriction factors belong to the TRIM (Tripartite Motif) family of proteins. These include the alpha isoform of TRIM5 (TRIM5α), a well characterized lentiviral restriction factor. However, given that there are at least seventy TRIM genes in the human genome, the specific functions of many TRIM proteins – let alone their primate orthologues – remain unknown. Until recently, this included non-human primate TRIM34, a paralog of the well-known TRIM5a.

In a new study published in Retrovirology, researchers from the Emerman Lab at Fred Hutch and Ohainle Lab at UC Berkeley reported that across multiple primate species, TRIM34 is a TRIM5-dependent restriction factor against many Simian Immunodeficiency Virus (SIV) capsids.

In a previous study, Dr. Molly Ohainle, then a staff scientist in Dr. Michael Emerman’s lab, used CRISPR-Cas9 screening to identify human TRIM34 as a restriction factor of some SIV capsids and of HIV-1 with a mutation in the N74D capsid. The new study “expanded on [Dr. Ohainle’s] previous work by looking at TRIM34 originating from both human and nonhuman primates, which is of relevance due to the zoonotic origins of HIV-1 and other related viruses,” said Joy Twentyman, a PhD candidate co-mentored by Drs. Ohainle and Emerman and the lead author of the new study.

The authors set out with an open-ended question: “Is TRIM34 from other primates a restriction factor, and if so, what are its targets?” They started by testing TRIM34 orthologues from human, chimpanzee, green monkey, and rhesus macaque against HIV-1 and SIV strains that arose from chimpanzees (SIVcpz), green monkeys (SIVagm-sab and SIVagm-tan), and rhesus macaques (SIVmac). The researchers generated a TRIM34-knockout human-cell line and overexpressed the TRIM34 orthologues with doxycycline-inducible lentiviral vectors, then infected the cells with HIV-1 and SIV capsids. They found that none of the four TRIM34 orthologues restricted HIV-1 or SIVcpz capsids, but that they all restricted SIVagm-sab, SIVagm-tan, and SIVmac capsids, suggesting that the antiviral activity of TRIM34 is conserved across primate species. “TRIM34 turns out to be somewhat different to TRIM5a, the other restriction factor that is involved in this work, in that TRIM5a has quite different restrictive capacity between species, whereas TRIM34 from different species seem to be broadly restrictive of a subset of viruses,” explained Twentyman.

Graphs depicting relative infectivity vs. human or macaque TRIM34 overexpression
The authors found that both human and rhesus macaque TRIM34 require human TRIM5a to restrict SIVagm-sab. In additional experiments, they found that primate TRIM34 orthologues can functionally interact with human TRIM5a, and that the SPRY domains of both TRIM34 and TRIM5a are critical to restriction. Overall, their results suggest TRIM34-mediated restriction is dependent on TRIM5. Image modified from Retrovirology article

Given this data, and that human TRIM34 requires TRIM5a to restrict HIV-1 N74D capsids, the researchers hypothesized that TRIM5a may be responsible for the specificity of TRIM34-mediated restriction. They found that both human and rhesus macaque TRIM34 require human TRIM5a to restrict SIVagm-sab, and that primate TRIM34 orthologues can functionally interact with human TRIM5a. Additionally, they found that the SPRY domains of both TRIM34 and TRIM5a are critical to restriction. Overall, their results suggest that TRIM5 confers a level of specificity to TRIM34-mediated restriction.

Twentyman said the results from this study have raised new questions about TRIM34 that are ripe for follow-up studies, including: “What is the determinant of antiviral specificity for TRIM34? What is the physical interaction between TRIM34 and TRIM5a like?  Are there downstream signaling events that occur subsequent to TRIM34-mediated restriction?”

The Ohainle lab, established in 2022 in the Department of Molecular and Cellular Biology at UC Berkeley, is well positioned to start interrogating these follow-up questions. According to Twentyman, “Molly is a great PI and she is taking postdocs!” Interested? You can learn more at the Ohainle Lab website:

The spotlighted work was supported by the National Institutes of Health.

Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium member Dr. Michael Emerman contributed to this work.

Twentyman J, Khalifeh A, Felton AL, Emerman M, Ohainle M. 2023. Primate TRIM34 is a broadly-acting, TRIM5-dependent lentiviral restriction factor. Retrovirology. 20(1):15.