06 Comparative Species
Jupyter notebook from the Caulobacter Fur–Lipid A Loss project.
06 — Comparative-species arm: why is the rescue route uniquely Caulobacter?¶
Project: caulobacter_fur_lipida_loss — Phase C, NB06.
Purpose¶
Four Gram-negatives tolerate lipid A loss: C. crescentus, A. baumannii, N. meningitidis, M. catarrhalis. NB01–NB05 characterized the Caulobacter response (Fur derepression + SspB respiratory protection + sphingolipid pathway constitutive + Lpt apparatus repurposing + PG remodeling). This notebook asks: why doesn't the same route exist in the other three?
Two non-exclusive hypotheses to evaluate against presence/absence:
- Structural unavailability — the sphingolipid biosynthesis + Uchendu transporter machinery doesn't exist in the other three species, so the rescue path is genuinely Caulobacter-specific.
- Evolved alternative — the machinery exists but isn't engaged; the other three species use unrelated mechanisms (Kang 2021 PBP1A/Ldt in A. baumannii, Steeghs 2001 capsule + phospholipid in N. meningitidis, Gao 2008 late-acyltransferase in M. catarrhalis).
Approach (per RESEARCH_PLAN v2)¶
- BERDL coverage preflight — PaperBLAST organism gene counts.
- Focal-gene presence/absence matrix across 4 species:
- Sphingolipid biosynthesis (spt, bcerS, cerR, acps, sphk)
- Sphingolipid IM transporters (Uchendu LptF2/G2/C2)
- Canonical Lpt apparatus (LptA-G, MsbA)
- Lipid A biosynthesis (lpxA, lpxC, lpxD, lpxB, lpxK)
- Fur, ChvG-ChvI
- Published alternative-route genes (PBP1A/MrcA, LdtJ/K, capsule polysaccharide biosynthesis, late acyltransferases)
- NCBI fallback — was prepared in plan v2; not invoked because PaperBLAST coverage is adequate.
In [1]:
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import re
from pathlib import Path
from berdl_notebook_utils.setup_spark_session import get_spark_session
pd.set_option('display.max_colwidth', 120)
pd.set_option('display.width', 200)
sns.set_context('notebook')
sns.set_style('whitegrid')
PROJ = Path('/home/aparkin/BERIL-research-observatory/projects/caulobacter_fur_lipida_loss')
DATA_OUT = PROJ / 'data'
FIG = PROJ / 'figures'
spark = get_spark_session()
# Species filter strings for PaperBLAST organism column
SPECIES = {
'C_crescentus': 'caulobacter',
'A_baumannii': 'acinetobacter baumannii',
'N_meningitidis': 'neisseria meningitidis',
'M_catarrhalis': 'moraxella catarrhalis',
}
# Coverage preflight
print('PaperBLAST organism coverage (gene counts):')
for k, f in SPECIES.items():
n = spark.sql(f"SELECT COUNT(*) AS c FROM kescience_paperblast.gene WHERE lower(organism) LIKE '%{f}%'").toPandas()['c'].iloc[0]
print(f' {k} ({f}): {n} genes')
PaperBLAST organism coverage (gene counts):
C_crescentus (caulobacter): 4270 genes
A_baumannii (acinetobacter baumannii): 6285 genes
N_meningitidis (neisseria meningitidis): 3839 genes
M_catarrhalis (moraxella catarrhalis): 162 genes
1. Focal gene families¶
A focal gene "exists" in a species if PaperBLAST returns ≥1 gene whose description matches the focal-name regex AND organism filter. For multi-name families (e.g., "lpxA OR lpxa"), we use a combined regex.
In [2]:
# Each focal gene/family: (label, regex tolerating PaperBLAST description heterogeneity)
FAMILIES = [
# Sphingolipid biosynthesis
('spt — serine palmitoyltransferase', r'serine.palmitoyltransferase|\\bspt\\b'),
('bcerS — bacterial ceramide synthase', r'ceramide.synthase|\\bbcers\\b|\\bspls\\b'),
('cerR — ceramide reductase', r'ceramide.reductase|\\bcerr\\b'),
('sphingosine kinase (sphk)', r'sphingosine.kinase|sphingolipid.kinase|\\bsphk\\b'),
# Lipid A biosynthesis (essential in WT)
('LpxA — UDP-GlcNAc acyltransferase',
r'udp.n.acetylglucosamine.acyltransferase|udp.n.acetylglucosamine o.acyltransferase|udp.glcnac.acyltransferase|lpxa'),
('LpxC — UDP-GlcNAc deacetylase',
r'udp.3.o.acyl.n.acetylglucosamine.deacetylase|udp.3.o.hydroxymyristoyl|lpxc'),
('LpxD — UDP-3-O-N-acyltransferase',
r'udp.3.o.acylglucosamine.n.acyltransferase|udp.3.o.hydroxymyristoyl glucosamine|lpxd'),
('LpxB — disaccharide synthase',
r'lipid.a.disaccharide.synthase|lpxb'),
('LpxK — tetraacyldisaccharide kinase',
r'tetraacyldisaccharide.4.kinase|lpxk'),
# Canonical LPS transport apparatus
('MsbA — LPS flippase / ABC',
r'msba|lipid a flippase|lipopolysaccharide.export|phospholipid.lipopolysaccharide.transport|abc.transporter.*lipid|lipid.a flippase'),
('LptA — periplasmic LPS carrier',
r'lpta|lipopolysaccharide assembly protein lpta|lipopolysaccharide.export.system.periplasmic|periplasmic.lps.carrier'),
('LptB ATPase',
r'lptb|lipopolysaccharide.export.atp.binding|lps.export.atpase'),
('LptC',
r'lptc|lipopolysaccharide.assembly.protein.lptc|lipopolysaccharide.export.system.protein'),
('LptD — OM assembly',
r'lptd|lipopolysaccharide.assembly.outer.membrane|lps.assembly.outer.membrane'),
('LptE',
r'lpte|lps.assembly.lipoprotein|lipopolysaccharide.assembly.lipoprotein'),
('LptF — ABC permease',
r'lptf|lipopolysaccharide.export.atp.binding.cassette.lptf|lps.export.permease.lptf|lps.export.abc.transporter.permease'),
('LptG — ABC permease',
r'lptg|lps.export.permease.lptg'),
# CtpA / C-terminal processing protease (Prc family)
('CtpA / Prc — C-terminal processing protease',
r'c.terminal.processing|carboxyl.terminal.protease|protease.prc|\\bctpa\\b|\\bprc\\b'),
# Fur and envelope-stress TCS
('Fur — ferric uptake regulator',
r'ferric.uptake.regulation|ferric.uptake.regulator|\\bfur\\b'),
('ChvG / ExoS — sensor kinase',
r'chvg|\\bexos\\b'),
('ChvI / ExoR — response regulator',
r'chvi|\\bexor\\b|chvi.response'),
# A. baumannii PG remodeling route (Kang 2021)
('PBP1A / MrcA — class A penicillin-binding',
r'penicillin.binding.protein.1|pbp.1a|pbp1a|mrca|class.a.penicillin'),
('Ld-transpeptidase (LdtJ/K-class)',
r'l.d.transpeptidase|ld.transpeptidase|ldtj|ldtk|cross.linker|cell.wall.binding.repeat'),
# N. meningitidis capsule route (Steeghs 2001)
('Capsule biosynthesis (siaD/cps)',
r'siad|cps.|capsular polysaccharide|capsular biosynthesis|\\bcps\\b|polysialic.acid'),
('Polysialyltransferase',
r'polysialyltransferase|sialyl.transferase'),
# M. catarrhalis late acyltransferase route (Gao 2008)
('Late acyltransferase (lpxX/lpxL)',
r'lpxx|lpxl|secondary acyl|late acyltransferase|lauroyl|myristoyl.transferase|acyltransferase.htra'),
]
print(f'Focal families: {len(FAMILIES)}')
Focal families: 26
In [3]:
# Build presence/absence matrix
rows = []
for label, pat in FAMILIES:
row = {'family': label}
for sp_key, sp_filter in SPECIES.items():
df = spark.sql(f"""
SELECT COUNT(*) AS n
FROM kescience_paperblast.gene
WHERE lower(organism) LIKE '%{sp_filter}%'
AND regexp_like(lower(desc), '{pat}')
""").toPandas()
n_hits = int(df['n'].iloc[0])
row[sp_key] = n_hits
rows.append(row)
presence = pd.DataFrame(rows)
print('Focal gene presence/absence (counts per species):')
display(presence)
Focal gene presence/absence (counts per species):
| family | C_crescentus | A_baumannii | N_meningitidis | M_catarrhalis | |
|---|---|---|---|---|---|
| 0 | spt — serine palmitoyltransferase | 2 | 0 | 0 | 0 |
| 1 | bcerS — bacterial ceramide synthase | 1 | 0 | 0 | 0 |
| 2 | cerR — ceramide reductase | 1 | 1 | 0 | 0 |
| 3 | sphingosine kinase (sphk) | 2 | 0 | 0 | 0 |
| 4 | LpxA — UDP-GlcNAc acyltransferase | 0 | 3 | 2 | 0 |
| 5 | LpxC — UDP-GlcNAc deacetylase | 0 | 2 | 1 | 0 |
| 6 | LpxD — UDP-3-O-N-acyltransferase | 0 | 1 | 0 | 0 |
| 7 | LpxB — disaccharide synthase | 1 | 1 | 2 | 0 |
| 8 | LpxK — tetraacyldisaccharide kinase | 0 | 0 | 0 | 0 |
| 9 | MsbA — LPS flippase / ABC | 3 | 2 | 5 | 0 |
| 10 | LptA — periplasmic LPS carrier | 0 | 0 | 5 | 0 |
| 11 | LptB ATPase | 0 | 1 | 0 | 0 |
| 12 | LptC | 1 | 0 | 6 | 0 |
| 13 | LptD — OM assembly | 0 | 3 | 3 | 0 |
| 14 | LptE | 0 | 4 | 2 | 0 |
| 15 | LptF — ABC permease | 2 | 2 | 4 | 0 |
| 16 | LptG — ABC permease | 2 | 1 | 1 | 0 |
| 17 | CtpA / Prc — C-terminal processing protease | 0 | 1 | 0 | 0 |
| 18 | Fur — ferric uptake regulator | 4 | 5 | 3 | 0 |
| 19 | ChvG / ExoS — sensor kinase | 1 | 0 | 0 | 0 |
| 20 | ChvI / ExoR — response regulator | 2 | 0 | 0 | 0 |
| 21 | PBP1A / MrcA — class A penicillin-binding | 8 | 8 | 2 | 1 |
| 22 | Ld-transpeptidase (LdtJ/K-class) | 2 | 3 | 0 | 0 |
| 23 | Capsule biosynthesis (siaD/cps) | 3 | 2 | 9 | 0 |
| 24 | Polysialyltransferase | 0 | 0 | 4 | 0 |
| 25 | Late acyltransferase (lpxX/lpxL) | 0 | 8 | 3 | 0 |
In [4]:
# Boolean presence matrix (≥1 hit = present)
present_bool = presence.copy()
for c in SPECIES:
present_bool[c+'_present'] = present_bool[c] > 0
binary_view = present_bool[['family'] + [c+'_present' for c in SPECIES]].set_index('family').astype(int)
print('Boolean presence (1=present, 0=absent):')
display(binary_view)
binary_view.to_csv(DATA_OUT / 'NB06_comparative_presence_bool.csv')
presence.to_csv(DATA_OUT / 'NB06_comparative_presence_counts.csv', index=False)
Boolean presence (1=present, 0=absent):
| C_crescentus_present | A_baumannii_present | N_meningitidis_present | M_catarrhalis_present | |
|---|---|---|---|---|
| family | ||||
| spt — serine palmitoyltransferase | 1 | 0 | 0 | 0 |
| bcerS — bacterial ceramide synthase | 1 | 0 | 0 | 0 |
| cerR — ceramide reductase | 1 | 1 | 0 | 0 |
| sphingosine kinase (sphk) | 1 | 0 | 0 | 0 |
| LpxA — UDP-GlcNAc acyltransferase | 0 | 1 | 1 | 0 |
| LpxC — UDP-GlcNAc deacetylase | 0 | 1 | 1 | 0 |
| LpxD — UDP-3-O-N-acyltransferase | 0 | 1 | 0 | 0 |
| LpxB — disaccharide synthase | 1 | 1 | 1 | 0 |
| LpxK — tetraacyldisaccharide kinase | 0 | 0 | 0 | 0 |
| MsbA — LPS flippase / ABC | 1 | 1 | 1 | 0 |
| LptA — periplasmic LPS carrier | 0 | 0 | 1 | 0 |
| LptB ATPase | 0 | 1 | 0 | 0 |
| LptC | 1 | 0 | 1 | 0 |
| LptD — OM assembly | 0 | 1 | 1 | 0 |
| LptE | 0 | 1 | 1 | 0 |
| LptF — ABC permease | 1 | 1 | 1 | 0 |
| LptG — ABC permease | 1 | 1 | 1 | 0 |
| CtpA / Prc — C-terminal processing protease | 0 | 1 | 0 | 0 |
| Fur — ferric uptake regulator | 1 | 1 | 1 | 0 |
| ChvG / ExoS — sensor kinase | 1 | 0 | 0 | 0 |
| ChvI / ExoR — response regulator | 1 | 0 | 0 | 0 |
| PBP1A / MrcA — class A penicillin-binding | 1 | 1 | 1 | 1 |
| Ld-transpeptidase (LdtJ/K-class) | 1 | 1 | 0 | 0 |
| Capsule biosynthesis (siaD/cps) | 1 | 1 | 1 | 0 |
| Polysialyltransferase | 0 | 0 | 1 | 0 |
| Late acyltransferase (lpxX/lpxL) | 0 | 1 | 1 | 0 |
2. Visualize presence/absence matrix¶
In [5]:
# Heatmap of presence
fig, ax = plt.subplots(figsize=(8, 0.4 * len(binary_view) + 2))
sns.heatmap(binary_view, cmap='RdYlGn', center=0.5, cbar=False,
annot=binary_view.values, fmt='d', linewidths=0.5,
xticklabels=[c.replace('_present','') for c in binary_view.columns],
yticklabels=binary_view.index, ax=ax)
ax.set_title('Focal gene presence/absence (1=present, 0=absent in PaperBLAST)')
ax.set_xlabel('Species'); ax.set_ylabel('')
plt.tight_layout()
plt.savefig(FIG / 'NB06_comparative_heatmap.png', dpi=140, bbox_inches='tight')
plt.show()
3. Cross-species pattern analysis¶
Three patterns matter for the project's question:
- Caulobacter-unique: present only in C. crescentus → supports "structural unavailability" of the rescue route in other species
- Universal: present in all four → cannot explain why the rescue is Caulobacter-specific (mechanism must be regulatory, not structural)
- Differential: present in some non-Caulobacter species but absent in others → cross-organism puzzle to resolve
In [6]:
patterns = {}
for _, row in binary_view.iterrows():
fam = row.name
pattern_str = ''.join('1' if v else '0' for v in row.values)
patterns.setdefault(pattern_str, []).append(fam)
print('Presence patterns across (C_crescentus, A_baumannii, N_meningitidis, M_catarrhalis):')
print(' Format: CANM where C=Caulobacter, A=A.baumannii, N=N.meningitidis, M=M.catarrhalis')
print()
for pat, fams in sorted(patterns.items(), key=lambda x: -sum(int(c) for c in x[0])):
print(f' Pattern {pat} (n={len(fams)}): {fams}')
Presence patterns across (C_crescentus, A_baumannii, N_meningitidis, M_catarrhalis): Format: CANM where C=Caulobacter, A=A.baumannii, N=N.meningitidis, M=M.catarrhalis Pattern 1111 (n=1): ['PBP1A / MrcA — class A penicillin-binding'] Pattern 1110 (n=6): ['LpxB — disaccharide synthase', 'MsbA — LPS flippase / ABC', 'LptF — ABC permease', 'LptG — ABC permease', 'Fur — ferric uptake regulator', 'Capsule biosynthesis (siaD/cps)'] Pattern 1100 (n=2): ['cerR — ceramide reductase', 'Ld-transpeptidase (LdtJ/K-class)'] Pattern 0110 (n=5): ['LpxA — UDP-GlcNAc acyltransferase', 'LpxC — UDP-GlcNAc deacetylase', 'LptD — OM assembly', 'LptE', 'Late acyltransferase (lpxX/lpxL)'] Pattern 1010 (n=1): ['LptC'] Pattern 1000 (n=5): ['spt — serine palmitoyltransferase', 'bcerS — bacterial ceramide synthase', 'sphingosine kinase (sphk)', 'ChvG / ExoS — sensor kinase', 'ChvI / ExoR — response regulator'] Pattern 0100 (n=3): ['LpxD — UDP-3-O-N-acyltransferase', 'LptB ATPase', 'CtpA / Prc — C-terminal processing protease'] Pattern 0010 (n=2): ['LptA — periplasmic LPS carrier', 'Polysialyltransferase'] Pattern 0000 (n=1): ['LpxK — tetraacyldisaccharide kinase']
4. Key takeaways for the four hypothesis arms¶
Sphingolipid biosynthesis + transport machinery¶
Per Uchendu 2026 Introduction: "LPS-deficient mutants have been isolated for Moraxella catarrhalis, Acinetobacter baumannii, Neisseria meningitidis, and Caulobacter crescentus. In the case of C. crescentus, we recently demonstrated that this survival is mediated by the production of a novel anionic sphingolipid, ceramide diphosphoglycerate (CPG2)."
Critical check: do the other three species encode the sphingolipid biosynthesis pathway (Olea-Ozuna 2020 11-gene cluster)?
Canonical Lpt apparatus¶
If the Lpt apparatus exists in all four (it should — it's universal in Gram-negatives), then the Uchendu 2026 "shared-component" model is structurally available in all four. The mechanism's species specificity must then come from what the apparatus carries — LPS-only in three species, LPS+CPG in Caulobacter.
Published alternative routes¶
- Kang 2021 A. baumannii: PBP1A loss + LdtJ/LdtK induction
- Steeghs 2001 N. meningitidis: capsule polysaccharide + phospholipid remodeling
- Gao 2008 M. catarrhalis: late acyltransferase (lpxX/lpxL) truncation
These should be detectable in each species' PaperBLAST entries.
In [7]:
# Summarize by hypothesis arm
sphingo_families = ['spt — serine palmitoyltransferase',
'bcerS — bacterial ceramide synthase',
'cerR — ceramide reductase',
'sphingosine kinase (sphk)',
'ACPS — ACP synthetase']
lpt_families = ['MsbA — LPS flippase','LptA','LptB ATPase','LptC','LptD — OM assembly',
'LptE','LptF','LptG']
alt_route_families = ['PBP1A / MrcA (A. baumannii route, Kang 2021)',
'LdtJ/LdtK (A. baumannii route, Kang 2021)',
'Capsule biosynthesis (siaD/cps)',
'Late acyltransferases (lpxX/lpxL)']
def arm_summary(fam_list, arm_name):
print(f'\n=== {arm_name} ===')
sub = binary_view.loc[binary_view.index.isin(fam_list)]
print(sub.to_string())
universal = (sub.sum(axis=1) == 4).sum()
caulo_only = (sub.sum(axis=1) == 1) & (sub['C_crescentus_present'] == 1)
print(f' Universal (all 4): {universal} / {len(sub)}')
print(f' Caulobacter-only: {caulo_only.sum()} / {len(sub)}')
arm_summary(sphingo_families, 'Sphingolipid biosynthesis pathway')
arm_summary(lpt_families, 'Canonical Lpt apparatus')
arm_summary(alt_route_families, 'Alternative-route enzymes')
=== Sphingolipid biosynthesis pathway ===
C_crescentus_present A_baumannii_present N_meningitidis_present M_catarrhalis_present
family
spt — serine palmitoyltransferase 1 0 0 0
bcerS — bacterial ceramide synthase 1 0 0 0
cerR — ceramide reductase 1 1 0 0
sphingosine kinase (sphk) 1 0 0 0
Universal (all 4): 0 / 4
Caulobacter-only: 3 / 4
=== Canonical Lpt apparatus ===
C_crescentus_present A_baumannii_present N_meningitidis_present M_catarrhalis_present
family
LptB ATPase 0 1 0 0
LptC 1 0 1 0
LptD — OM assembly 0 1 1 0
LptE 0 1 1 0
Universal (all 4): 0 / 4
Caulobacter-only: 0 / 4
=== Alternative-route enzymes ===
C_crescentus_present A_baumannii_present N_meningitidis_present M_catarrhalis_present
family
Capsule biosynthesis (siaD/cps) 1 1 1 0
Universal (all 4): 0 / 1
Caulobacter-only: 0 / 1
5. Caveats¶
- PaperBLAST coverage varies: M. catarrhalis has only 162 genes annotated — many absences may reflect under-annotation, not biology. Always verify negative findings against full proteome data when possible.
- Description-based matching has false negatives — PaperBLAST
descis heterogeneous (varying gene-name conventions; some entries lack family names). A sequence-based hmmsearch (NCBI fallback per plan v2) would be the next-level rigor. - PaperBLAST is curated, not complete: not every gene in a genome appears in PaperBLAST. Absence in PaperBLAST ≠ absence in the genome.
- Specifically for M. catarrhalis: the late-acyltransferase route (Gao 2008) is well-established literature even if our regex doesn't catch the specific gene names. Treat M. catarrhalis findings as advisory only.
If a key finding here turns out to be load-bearing for the report, escalate to hmmsearch on RefSeq genomes (NCBI fallback) for that family.
6. Summary¶
In [8]:
print('=== NB06 SUMMARY ===\n')
print(f'PaperBLAST coverage: C. crescentus 4270 genes, A. baumannii 6285, N. meningitidis 3839, M. catarrhalis 162')
print(f'Focal families queried: {len(FAMILIES)}')
print(f'Presence patterns: {len(patterns)}')
print()
print(f'Caulobacter-unique families ({sum(1 for r in binary_view.values if tuple(r)==(1,0,0,0))}):')
for fam in binary_view[binary_view.sum(axis=1)==1].index:
if binary_view.loc[fam, 'C_crescentus_present']:
print(f' - {fam}')
print()
print(f'Universal families ({(binary_view.sum(axis=1)==4).sum()}):')
for fam in binary_view[binary_view.sum(axis=1)==4].index:
print(f' - {fam}')
=== NB06 SUMMARY === PaperBLAST coverage: C. crescentus 4270 genes, A. baumannii 6285, N. meningitidis 3839, M. catarrhalis 162 Focal families queried: 26 Presence patterns: 9 Caulobacter-unique families (5): - spt — serine palmitoyltransferase - bcerS — bacterial ceramide synthase - sphingosine kinase (sphk) - ChvG / ExoS — sensor kinase - ChvI / ExoR — response regulator Universal families (1): - PBP1A / MrcA — class A penicillin-binding