NLRX1 (NLR family member X1; NOD5/NOD9; CLR11.3) — review notes

UniProt: Q86UT6 (NLRX1_HUMAN), 975 aa precursor, HGNC:29890. N-terminal mitochondrial
transit peptide (1-86); NACHT NTPase domain (160-483); C-terminal LRR region (667-975).
Homohexamer (homodimers trimerize). PDB 3UN9 (LRR/RNA-binding element).

Summary of function

NLRX1 is an atypical NOD-like receptor (NLR) that, unlike most NLRs, localizes to the
mitochondrion (outer membrane, with the transit peptide targeting it to mitochondria;
the C-terminal LRR has an RNA-binding element). It is a mitochondrial regulator that sits
at the intersection of antiviral signaling, autophagy/mitophagy, ROS, and inflammasome
control.

Core/established functions:
1. Negative regulation of MAVS-mediated (RIG-I/RLH) antiviral signaling. NLRX1 localizes
to the mitochondrial outer membrane and interacts with MAVS, inhibiting the virus-induced
RIG-I-like-helicase-MAVS interaction and dampening type I interferon induction
PMID:18200010.
2. Promotion of autophagy via TUFM. NLRX1 binds the mitochondrial elongation factor TUFM,
which in turn recruits the autophagy proteins ATG5-ATG12 (ATG16L1), linking NLRX1 to
autophagy induction and modulation of type I IFN [UniProt FUNCTION; PMID:22749352
"The mitochondrial proteins NLRX1 and TUFM form a complex that regulates type I interferon and autophagy"].
The TUFM interaction is also captured by the cached PMID:28611246 (TUFM as a host
restriction factor against avian influenza, correlated with autophagy), where NLRX1-TUFM
is the IPI partner in the GOA. NLRX1 is thus a mitochondrial regulator of autophagy/mitophagy
(TUFM/ATG5-ATG12).
3. Regulation of MAVS-dependent NLRP3 inflammasome activation / attenuation of apoptosis
and inflammation. NLRX1 inhibits MAVS-dependent NLRP3 inflammasome activation, reducing
IL-1beta/IL-18/IL-6 and apoptosis (shown in myocardial ischemia)
PMID:27393910.
4. ROS and NF-kB/JNK modulation. NLRX1 has no inhibitory function on NF-kB itself but
amplifies NF-kB and JNK signaling through ROS production [UniProt FUNCTION; PMID:18219313].
Note the GOA carries an IBA "negative regulation of canonical NF-kappaB signal transduction"
transferred from the mouse ortholog - this is contested (UniProt explicitly states NLRX1
"Has no inhibitory function on NF-kappa-B signaling pathway, but enhances NF-kappa-B and
JUN N-terminal kinase dependent signaling through the production of reactive oxygen species").

Localization

Mitochondrion / mitochondrial outer membrane (transit peptide; multiple EXP/IDA/HTP/IBA/TAS).
The Reactome cytosol annotation (R-HSA-9749471, "NLRX1 binds CHUK:IKBKB:IKBKG") reflects a
pathway-step model; NLRX1's dominant localization is the mitochondrion. Mitochondrion is the
core compartment.

Annotation assessment highlights

• Mitochondrial outer membrane (GO:0005741) and mitochondrion (GO:0005739): ACCEPT (core),
  across EXP/IDA/IBA/HTP/TAS evidence.
• negative regulation of RIG-I signaling pathway (GO:0039536, IBA): ACCEPT - core antiviral
  function (corroborated by experimental PMID:18200010 disrupting RLH-MAVS).
• negative regulation of canonical NF-kappaB signal transduction (GO:0043124, IBA): contested.
  UniProt (human) says NLRX1 has no inhibitory NF-kB function and instead enhances NF-kB via
  ROS. The IBA term is transferred from the mouse ortholog. Given the human-specific UniProt
  statement and that this is an unverified phylogenetic inference, mark MARK_AS_OVER_ANNOTATED
  (do not REMOVE - the mouse ortholog evidence is real and per guidelines IBA over-propagation
  can be argued against but the direction is genuinely disputed in the literature).
• protein binding (GO:0005515) IPI with TUFM (PMID:28611246) and SARM1 (PMID:21903422):
  KEEP_AS_NON_CORE; the TUFM interaction underpins the autophagy function but bare protein
  binding is uninformative.
• cytosol (GO:0005829 TAS Reactome): KEEP_AS_NON_CORE (pathway-step; mitochondrion is core).

Functions NOT yet annotated (candidate NEW)

• Interaction with TUFM and recruitment of ATG5-ATG12 to promote autophagy (PMID:22749352)
  is in UniProt FUNCTION but not yet a GO BP annotation in the GOA - candidate for a
  positive regulation of autophagy / regulation of mitophagy NEW annotation.
• negative regulation of MAVS/type I IFN is the experimental core (PMID:18200010) but the
  GOA only carries the IBA RIG-I term and Reactome.