Nitratidesulfovibrio vulgaris Pathways Project

Nitratidesulfovibrio vulgaris Pathways Project

Overview

This project focuses on reviewing gene annotations for key pathways in Nitratidesulfovibrio vulgaris (formerly Desulfovibrio vulgaris, strain Hildenborough). This sulfate-reducing bacterium is a model organism for studying anaerobic respiration using sulfate as the terminal electron acceptor.

Model Organism

Species: Nitratidesulfovibrio vulgaris (strain Hildenborough)

Pathway 1: Sulfate Reduction

The dissimilatory sulfate reduction pathway is the core energy metabolism of this organism. Sulfate is reduced to sulfide in a multi-step process:

  1. Sulfate uptake - via sulfate permeases
  2. Sulfate activation - ATP sulfurylase generates adenylyl-sulfate (APS)
  3. APS reduction - APS reductase (AprAB) reduces APS to sulfite
  4. Electron transfer - QmoABC complex links APS reduction to quinone pool

Genes for Review

Locus Gene UniProt ID Protein
DVU0846 aprB Q72DT3 Adenylylsulfate reductase, beta subunit
DVU0847 aprA Q72DT2 Adenylylsulfate reductase, alpha subunit
DVU0848 qmoA Q72DT1 Quinone-interacting membrane-bound oxidoreductase
DVU0849 qmoB Q72DT0 Quinone-interacting membrane-bound oxidoreductase
DVU0850 qmoC Q72DS9 Quinone-interacting membrane-bound oxidoreductase
DVU0279 Q72FD5 Sulfate permease family protein

Pathway 2: Potassium Transport

Potassium homeostasis is critical for maintaining membrane potential and osmotic balance.

Genes for Review

Locus Gene UniProt ID Protein
DVU1606 Q72BM9 Potassium uptake protein, TrkA family
DVU3335 Q725U0 Sensory box histidine kinase
DVU3336 kdpD Q725T9 Potassium channel histidine kinase domain protein
DVU3337 kdpC Q725T8 Potassium-transporting ATPase, C subunit
DVU3338 kdpB Q725T7 Potassium-transporting ATPase, B subunit (ATP-binding)
DVU0412 Q72F06 Potassium uptake protein TrkA, putative
DVU0413 trkH Q72F05 Potassium uptake protein, TrkH family

Pathway 3: Sigma Factors

Sigma factors regulate gene expression by directing RNA polymerase to specific promoters.

Genes for Review

Locus Gene UniProt ID Protein
DVU1584 rpoH Q72BQ0 RNA polymerase sigma-70 factor (heat shock)
DVU1628 rpoN Q72BK7 RNA polymerase sigma-54 factor
DVU1788 rpoD Q72B50 RNA polymerase sigma-70 factor (housekeeping)
DVU2929 rpoC Q727C6 DNA-directed RNA polymerase, beta prime subunit
DVU3229 fliA Q726C4 RNA polymerase sigma factor for flagellar operon

Pathway 4: Hydrogen Metabolism

D. vulgaris Hildenborough possesses multiple hydrogenases for hydrogen cycling, which is central to its energy metabolism. The organism has four periplasmic hydrogenases for H2 uptake and two membrane-bound cytoplasmic hydrogenases for H2 production.

Periplasmic Hydrogenases (H2 Uptake)

Locus Gene UniProt ID Protein
DVU1769 hydA P07598 [Fe] hydrogenase large subunit
DVU1770 hydB P07603 [Fe] hydrogenase small subunit
DVU1917 hysB Q72AS4 [NiFeSe] hydrogenase small subunit
DVU1918 hysA Q72AS3 [NiFeSe] hydrogenase large subunit
DVU1921 hynB1 Q06173 [NiFe] hydrogenase 1 small subunit
DVU1922 hynA1 Q72AS0 [NiFe] hydrogenase 1 large subunit

Membrane-Bound Cytoplasmic Hydrogenases (H2 Production)

Locus Gene UniProt ID Protein
DVU0434 echA Q72EY4 Ech hydrogenase, subunit EchA (catalytic)
DVU0433 echB Q72EY5 Ech hydrogenase, subunit EchB
DVU2291 cooH Q729Q8 Coo hydrogenase, CooH subunit (catalytic)
DVU2287 cooK Q729R2 Coo hydrogenase, CooK subunit (selenocysteine)

Genes for Initial Review (Representative Subunits)

Locus Gene UniProt ID Protein
DVU1769 hydA P07598 [Fe] hydrogenase large subunit (catalytic)
DVU1918 hysA Q72AS3 [NiFeSe] hydrogenase large subunit (catalytic)
DVU1922 hynA1 Q72AS0 [NiFe] hydrogenase 1 large subunit (catalytic)
DVU0434 echA Q72EY4 Ech hydrogenase, subunit EchA (catalytic)
DVU2291 cooH Q729Q8 Coo hydrogenase, CooH subunit (catalytic)

Key References

STATUS

Sulfate Reduction Pathway (Priority 1) - COMPLETED

Sigma Factors (Priority 3) - COMPLETED

Potassium Transport (Priority 2) - COMPLETED

Hydrogen Metabolism (Priority 4) - IN PROGRESS

NOTES

2026-01-15

Project created. Compiled gene list for three pathways in Nitratidesulfovibrio vulgaris (Hildenborough):

  1. Sulfate reduction pathway (6 genes) - Core energy metabolism
  2. APS reductase complex (AprAB): DVU0846-0847
  3. QmoABC complex: DVU0848-0850

  4. Sulfate permease: DVU0279

  5. Potassium transport (7 genes) - Ion homeostasis

  6. TrkA/TrkH systems: DVU0412-0413, DVU1606
  7. Kdp system (ATP-driven): DVU3336-3338

  8. Regulatory kinase: DVU3335

  9. Sigma factors (5 genes) - Transcriptional regulation

  10. Housekeeping (RpoD), heat shock (RpoH), nitrogen (RpoN), flagellar (FliA)
  11. Note: RpoC is RNA polymerase subunit, not a sigma factor

Priority: Start with sulfate reduction pathway as this is the defining metabolic feature of this organism.

All UniProt IDs retrieved from UniProt REST API using DVU locus tags. Note that the organism name has been updated from Desulfovibrio vulgaris to Nitratidesulfovibrio vulgaris but UniProt IDs remain valid.

Sulfate Reduction Pathway Reviews Completed:

Key findings from annotation reviews:

  1. AprAB (APS Reductase):
  2. aprB (Q72DT3): Beta subunit with two [4Fe-4S] clusters. Core function is electron transfer (GO:0009055), not catalytic activity. Modified GO:0009973 (adenylyl-sulfate reductase activity) to electron transfer activity since AprB is the electron relay, not the catalytic subunit.

  3. aprA (Q72DT2): Alpha subunit containing FAD. This is the catalytic subunit. Accepted GO:0009973 (adenylyl-sulfate reductase activity). Added GO:0019420 (dissimilatory sulfate reduction).

  4. DVU0848-0850 (NOT QmoABC!):

  5. CRITICAL FINDING: DVU0848-0850 are actually part of the FlxABCD-HdrABC electron bifurcating complex, NOT the QmoABC complex as initially annotated in the input list.
  6. DVU0848 (Q72DT1): HdrA-like protein with FAD/NAD-binding domains. Functions in electron bifurcation, coupling NADH oxidation with ferredoxin reduction. Essential for ethanol metabolism.
  7. DVU0849 (Q72DT0): HdrA/FAD-containing subunit of the Flx-Hdr complex.

  8. DVU0850 (Q72DS9): This IS QmoC - the membrane-integral subunit with heme b groups that transfers electrons from the quinone pool. Part of the actual QmoABC complex.

  9. DVU0279 (Q72FD5) - Sulfate Permease?:

  10. ANNOTATION CONCERN: Despite being annotated as "sulfate permease family protein", the SulP/SLC26 family is functionally diverse. Many members transport dicarboxylates, bicarbonate, or other anions rather than sulfate. The annotation GO:0055085 (transmembrane transport) was accepted but sulfate-specific transport needs experimental verification.

Sigma Factor Pathway Reviews Completed:

Key findings from annotation reviews:

  1. rpoC (Q727C6) is NOT a sigma factor:

  2. CRITICAL CORRECTION: rpoC encodes the RNA polymerase beta' (β') subunit, which is the DNA-binding core subunit of RNAP - NOT a sigma factor. This was incorrectly listed in the original gene set. RpoC provides DNA template binding and forms part of the catalytic core enzyme.

  3. Sigma factor family classification:

  4. rpoH (Q72BQ0): Sigma-32 family (σ32), heat shock response
  5. rpoN (Q72BK7): Sigma-54 family (σ54), nitrogen regulation and alternative metabolism
  6. rpoD (Q72B50): Sigma-70 family (σ70), housekeeping transcription

  7. fliA (Q726C4): Sigma-28 family (σ28), flagellar gene expression

  8. Over-annotation patterns:

  9. Many sigma factors had GO:0003700 (DNA-binding transcription factor activity) which is incorrect - sigma factors recognize promoters but do not bind DNA themselves; the DNA-binding is performed by the RNAP core enzyme.
  10. Proposed replacement with GO:0016987 (sigma factor activity).

Potassium Transport Pathway Reviews Completed:

Key findings from annotation reviews:

  1. Two distinct K+ transport systems identified:
  2. KdpFABC system (DVU3335-3338): High-affinity ATP-driven K+ pump induced under K+ limitation

  3. Trk/Ktr system (DVU0412-0413, DVU1606): Constitutive K+ uptake channels

  4. KdpFABC Complex - Functional assignments:

  5. kdpB (Q725T7): P-type ATPase motor - the ONLY subunit with catalytic activity. Contains the catalytic aspartate D307 that cycles through phosphorylation. Annotated with GO:0008556 (P-type K+ transporter activity).
  6. kdpC (Q725T8): Catalytic chaperone - does NOT have ATPase activity! Incorrectly annotated with ATP binding and hydrolase activity. Its actual function is GO:0001671 (ATPase activator activity) - it increases KdpB's ATP-binding affinity.
  7. kdpD (Q725T9): Tandem serine-histidine kinase sensor that controls KdpFABC expression in response to K+ levels and turgor.

  8. DVU3335 (Q725U0): KdpE-like response regulator partnered with KdpD for two-component signaling.

  9. Trk/Ktr System - Pore vs Regulator distinction:

  10. trkH (Q72F05): Membrane channel pore - this is the actual K+ transporter with transmembrane domains.
  11. DVU0412 (Q72F06) and DVU1606 (Q72BM9): Cytosolic RCK (regulator of K+ conductance) regulatory subunits. These do NOT transport ions themselves - they form octameric gating rings that regulate the TrkH channel through ATP/ADP-dependent conformational changes.

  12. Key correction: Both TrkA proteins were incorrectly annotated with GO:0008324 (transporter activity). They should have GO:0015459 (potassium channel regulator activity).

  13. c-di-AMP signaling:

  14. The second messenger c-di-AMP binds to RCK regulatory subunits to modulate K+ uptake capacity, linking potassium homeostasis to broader cellular signaling networks.