Genome sequences of Arthrobacter spp. that use a modified sulfoglycolytic Embden-Meyerhof-Parnas pathway

Abstract

Sulfoglycolysis pathways enable the breakdown of the sulfosugar sulfoquinovose and environmental recycling of its carbon and sulfur content. The prototypical sulfoglycolytic pathway is a variant of the classical Embden-Meyerhof-Parnas (EMP) pathway that results in formation of 2,3-dihydroxypropanesulfonate and was first described in gram-negative Escherichia coli. We used enrichment cultures to discover new sulfoglycolytic bacteria from Australian soil samples. Two gram-positive Arthrobacter spp. were isolated that produced sulfolactate as the metabolic end-product. Genome sequences identified a modified sulfoglycolytic EMP gene cluster, conserved across a range of other Actinobacteria, that retained the core sulfoglycolysis genes encoding metabolic enzymes but featured the replacement of the gene encoding sulfolactaldehyde (SLA) reductase with SLA dehydrogenase, and the absence of sulfoquinovosidase and sulfoquinovose mutarotase genes. Excretion of sulfolactate by these Arthrobacter spp. is consistent with an aerobic saprophytic lifestyle. This work broadens our knowledge of the sulfo-EMP pathway to include soil bacteria.

Keywords: Enrichment; Isotope labeling; Nuclear magnetic resonance spectroscopy; Sulfur cycle.

Fig. 1

Scanning electron microscopy image of Arthrobacter sp. a strain AK01, b strain AK04. Cell morphology was examined using a scanning electron microscope (Quanta 200 ESEM). Cells were grown in LB media for 3 days, fixed in 0.05% glutaraldehyde in 0.1 M phosphate buffer (pH 7.4), then in 2.5% glutaraldehyde in 0.1 M phosphate buffer (pH 7.4) and allowed to react for 20 min. Fixed cells were adhered onto poly-lysine-coated slides and rinsed with water 3 times, then dehydrated by soaking in an ascending ethanol gradient (20–100%). The sample was critical point dried using a Leica CPD3000 and gold coated to thickness of 5 nm using Safematic CCU-010 compact coating unit. Images are at approximately 50,000 × magnification with scale bar shown

Fig. 2

Proposed sulfoglycolytic Embden–Meyerhof–Parnas (sulfo-EMP) pathway for Arthrobacter spp. a Gene cluster encoding the sulfo-EMP pathway for Arthrobacter sp. AK04. b Gene cluster encoding the sulfo-EMP pathway for Arthrobacter sp. AK01. c Proposed sulfo-EMP pathway for Arthrobacter spp. d Comparison with EMP pathway for E. coli K12

Fig. 3

Growth curves of Arthrobacter strains a AK01 and c AK04 grown on minimal salts media containing 5 mM glucose or SQ. ¹³C-NMR (500 MHz) spectra of spent culture media of Arthrobacter strains b AK01 and d AK04 grown on ¹³C₆-SQ (7.7 mM)

Fig. 4

Distribution and architecture of sulfo-EMP gene clusters in Arthrobacter and related organisms. Syntenic relationship of sulfo-EMP gene clusters in Arthrobacter sp. AK01 and AK04 with homologous gene clusters. Colored links indicate ≥ 30% protein sequence similarity. Genome accession codes: Arthrobacter sp. D2 (LUKB01000109.1), Arthrobacter sp. D4 (LUKC01000078.1), Arthrobacter sp. AAC2 (JAAGBD010000014.1), Arthrobacter sp. M5 (LVCB01000107.1), Arthrobacter sp. M6 (LVCC01000103.1), Arthrobacter sp. AK-YN10 (AVPD02000157.1), Arthrobacter sp. ATCC 21,022 (CP014196.1) Arthrobacter sp. EpRS71 (LNUV01000003.1), Arthrobacter sp. ZXY-2 (CP017421.1), Arthrobacter sp. AG367 (VIVE01000010.1), Arthrobacter sp. AG258 (SOBI01000009.1), Arthrobacter sp. 4J27 (CAQI01000048.1), Arthrobacter sp. S39 (SIHX01000007.1), Arthrobacter sp.1704 (SOBD01000016.1), Arthrobacter sp. BB-1 (VDEV01000010.1), Arthrobacter sp. FB24 (CP000454.1), Arthrobacter sp. KBS0703 (MVDG02000001.1), Arthrobacter sp. OV608 (FOEZ01000003.1), Arthrobacter sp. PGP41 (CP026514.1), Arthrobacter sp. SLBN-53 (VFMZ01000001.1), Arthrobacter sp. SLBN-83 (VFMX01000001.1), Arthrobacter sp. SLBN-112 (VFMU01000001.1), Arthrobacter sp. SLBN-122 (VFMS01000001.1), Arthrobacter sp. SLBN-179 (VFNR01000001.1), Arthrobacter sp. Soil761 (LMSF01000007.1), Arthrobacter sp. Soil764 (LMSI01000008.1), Pseudarthrobacter phenanthrenivorans (CP002379.1), Pseudarthrobacter phenanthrenivorans (RBNH01000003.1), Pseudarthrobacter phenanthrenivorans (VHJD01000009.1), Pseudarthrobacter sp. AG30 (QEHL01000024.1), Arthrobacter sp. MYb23 (PCPR01000010.1), Arthrobacter sp. KBS0703 (MVDG02000001.1), Microbacterium sp. No. 7 (CP012697.1), Acrocarpospora corrugata (BLAD01000050.1), Phytohabitans houttuyneae (BLPF01000004.1), Pseudoruegeria haliotis (PVTD01000003.1)