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Organism

Caulobacter crescentus

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Projects cited
3 project reports, listed in the margin
Relations
supports 2refines 2
Linked from
6 pages3 topics

What this entity is

Canonical name: Caulobacter crescentus 1

Known alias: C. crescentus 1

Stable external identifier: No stable external identifier was reported in this document. 1

Caulobacter crescentus is the alphaproteobacterial model in which combined loss of fur and sspb permits viability after deletion of lpxc, a lipid A-biosynthesis gene. 1

Findings in the lipid A-loss study

The 4584-vs-4580 contrast, representing Δfur ΔsspB ΔrsaA versus ΔrsaA, correlated with Leaden 2018’s Δfur signal across 93 differentially expressed genes with Spearman ρ = 0.315, p = 2.08e-03, and 71% sign concordance. 1

Of those 93 genes, 53 were buffered in the present data, with logFC approximately 0 despite Leaden values of -5 to -9; the buffered set was dominated by the cbb3/cyd/fix-NOPQ micro-aerobic respiratory operon, including CCNA_01466-01476, ccoNOPQ, cydCDA, and fixG/H/I. 1

The study therefore supports fur derepression in C. crescentus, while the mechanistic importance of the ΔsspB-buffered respiratory program for Δlpxc rescue remains a hypothesis. 1

The C. crescentus RB-TnSeq compendium in kescience-fitnessbrowser covered 198 experiments, including 22 envelope-stress experiments and zero iron-limitation experiments. 1

Among 3943 genes, 1311 had phenotype-bearing genes in the genome-wide envelope-stress background, or 33.25%. 1

The 32-gene concordant-strong Fur signature contained 17 phenotype-bearing genes, or 53.1%, corresponding to 1.60× enrichment with hypergeometric p = 0.016, whereas the 26-gene SspB-buffered set contained 9 phenotype-bearing genes, or 34.6%, corresponding to 1.04× enrichment with p = 0.515. 1

ChvT (CCNA_03108) had envelope-stress |t| = 43.7, while other Fur-derepressed TBDTs included CCNA_02910, CCNA_00210, CCNA_02048, and CCNA_00028 with |t| values of 9-28. 1

Published chvi-induced regulons contained 488 genes in the tested universe and partitioned into 20 unique-to-early genes, 10 genes induced in both phases, and 49 late-consequence genes, for a disjoint total of 79 induced genes. 1

The both-phases group included ChvI itself, CCNA_00237, which had logFC +1.45 in the 4584-vs-4580 contrast, supporting ChvI autoregulation. 1

The late-consequence group included LolA-family CCNA_03820 at +2.89, Pal-like CCNA_00784 at +2.08, a zot-like membrane perturber, osrP, and multiple TBDTs. 1

The sphingolipid-biosynthesis pathway was constitutive rather than induced: 0/6 biosynthesis genes were UP, spt was DOWN by -0.64 with FDR 0.002, and sphk was DOWN by -0.40 with FDR 0.02. 1

This constitutive sphingolipid-substitution route is linked to sphingolipid biosynthesis and is contrasted with the lipid A-loss pathways identified in the comparator species. 1

CtpA/CCNA_03113 showed logFC +0.58 with pvalue = 0.048 and FDR = 0.109 in 4599-vs-4584, was not detected in the outer-membrane proteome, and was rejected at the preregistered bar. 1

No canonical Lpt component was DOWN at the transcript level; the MsbA-like CCNA_00307 was UP by +0.89 with FDR 0.01, and LptC-related CCNA_03716 was UP by +0.56 with FDR 0.005. 1

At the protein level, LptD changed by log2(4672/4659) = -0.47 and by log2(4672/4580) = -0.62, while LptE changed by -0.78 and -0.68, respectively. 1

The sphingolipid transporter CCNA_01226 (lptC2) showed transcript -0.60 with FDR 0.034 but protein log2(4672/4659) = +1.08, corresponding to a net protein change of +0.66 log2, or approximately 1.58×, versus the wild-type baseline. 1

The peptidoglycan-remodeling set contained 53 loci, of which 28 unique loci met the H4 threshold; 25 were transcript-significant in 4599-vs-4584 at FDR<0.05 and 6 had outer-membrane-proteome |log2|>1. 1

The response contained 20 DOWN loci, 5 UP transcript hits, and 3 UP protein hits. 1

Specific induced activities included SdpA/CCNA_01252 at +4.8 log2 protein, Pal/CCNA_00784 at +2.08 transcript and +2.84 protein, PleA, PbpX, and CCNA_01754. 1

Basal division and elongation machinery was broadly reduced, including FtsI, PbpZ at -1.08 transcript, PbpC at -1.15 protein, a D,D-transpeptidase at -1.27 protein, murD, mviN/murJ, multiple LdpD/E/F M23-family endopeptidases, amiC, ripA, and membrane-bound transglycosylase A at -2.47 log2 protein. 1

Pal was induced at both transcript and protein levels and was also among the late-cohort ChvI genes; the report interprets tol pal system upregulation as consistent with increased lipid-remodeling demand after loss of outer-leaflet lipid A. 1

Metabolic context

A related GapMind pilot, a computational pathway-completeness method, included Caulobacter vibrioides (“Caulo”) among seven organisms and found 18/18 amino-acid biosynthesis pathways complete, or 100%, in that organism. This supports the interpretation that the Caulobacter model has broad biosynthetic capacity, but the result is computational, concerns C. vibrioides as named in that report, and does not establish that any pathway is essential for viability in C. crescentus. 2

The pathway-capability analysis refines this comparison by including C. crescentus among seven Tier 1 organisms matched between Fitness Browser fitness data and GapMind predictions; only 7 of the 48 Fitness Browser organisms had matching GapMind genome data. 3 It classified 161 organism–pathway pairs across those seven organisms by combining pathway completeness with gene-level fitness evidence, demonstrating that genomic capability and experimentally observed dependency are distinct rather than interchangeable. 3

The pilot also found fumarate and succinate, acetate, propionate, and L-lactate, all amino acids, deoxyribose and deoxyribonate, and putrescine conserved as carbon sources across all 7 organisms. This refines the envelope-focused picture with a small-sample metabolic comparison rather than evidence for a specific lipid A-loss mechanism. 2

The newer analysis further supports a condition-dependent interpretation of metabolic fitness: all 66 aggregate Latent Capability pairs became fitness-important under at least one condition type, although its median-based condition-specific threshold can cause reclassification by construction and requires independent calibration. 3

Comparative context and limitations

NCBI annotation found that spt and cerR were restricted to C. crescentus across C. crescentus, acinetobacter baumannii, neisseria meningitidis, and moraxella catarrhalis, with pattern 1000. 1

chvg and chvi also showed pattern 1000, supporting restriction of the ChvG–ChvI circuit to C. crescentus among the tested species. 1

The original kescience-paperblast screen returned 0 hits for LpxA versus 11 NCBI hits, 0 versus 15 for LpxC, 0 versus 15 for LpxD, 0 versus 15 for LpxB, and 0 versus 18 for LpxK, which the report characterized as an approximately 80% false-negative rate for the tested C. crescentus lipid A genes. 1

The study had single-replicate outer-membrane proteomics, so the lptC2 protein induction, Pal–Tol upregulation, LptD/LptE decline, and CCNA_01217 increase require replicated proteomics before publication-level claims can be made. 1

The study also lacked iron-limitation experiments in its 198-experiment fitness compendium, leaving the iron-axis component of the rescue mechanism unresolved. 1

The metabolic comparison likewise has limited scope: only 7 organisms were mapped successfully from an underlying collection of 45, and GapMind predictions are computational and may miss non-canonical or divergent pathways. The newer pathway analysis also covered only 80 pathways—18 amino acid biosynthesis pathways and 62 carbon-source utilization pathways—and used KEGG-based mapping, which can miss genes lacking KEGG annotations. These limitations refine rather than resolve questions about condition-specific metabolic essentiality in C. crescentus. 2 3

Projects cited

  1. Regulatory and proteomic architecture of Δfur-permitted lipid A loss in *Caulobacter crescentus*caulobacter_fur_lipida_loss · cited 30× · primary source
  2. Essential Metabolome: GapMind Pathway Analysis Across Essential-Gene Organismsessential_metabolome · cited 3× · supports · refines
  3. Metabolic Capability vs Dependencypathway_capability_dependency · cited 4× · refines · supports