Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum

Abstract

The genus Desulfonema belongs to the deltaproteobacterial family Desulfobacteraceae and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of Dn. limicola 5ac10T (6.91 Mbp; 6,207 CDS) and Dn. magnum 4be13T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other Desulfobacteraceae members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of Dn. limicola and Dn. magnum have the following general characteristics: 98 versus 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 versus 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The Dn. magnum typifying capacity for aromatic compound degradation (e.g., p-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in Dn. limicola). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69-96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both Desulfonema strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of Dn. limicola and Dn. magnum to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.

Keywords: Anaerobic degradation; Aromatic compounds; Complete genome; Desulfonema limicola; Desulfonema magnum; Differential proteomics; Metabolism; Physiology; Stress response; Sulfate reduction.

Fig. 1

Structural representation of the circular chromosomes of Desulfonema limicola 5a10^T (top) and Desulfonema magnum 4be13^T (bottom). The insert defines the color coding of rings for the selected functions. The scale (Mbp) is indicated by the outer ring. Chemical structures of growth supporting aromatic and aliphatic compounds are presented at the outside. Compound numbering is as follows: 1, 4-hydroxybenzoate; 2, benzoate; 3, p -cresol; 4, 3-phenylpropionate; 5, phenylacetate; 6, n -propanol; 7, propionate; 8, succinate; 9, fumarate; 10, malate; 11, lactate; 12, butyrate; 13, valerate; 14, acetate; 15, carbon dioxide.

Fig. 2

Proteogenomic datasets for Dn. limicola and Dn. magnum a Distribution of coding sequences and their proteomic coverage across the clusters of orthologous groups of proteins (COG). COG categories (in alphabetic order): A, RNA processing and modification; B, chromatin structure and dynamics; C, energy production and conservation; D, cell cycle control, cell division, chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination, repair; M, cell wall/membrane/envelope biogenesis; N, cell motility; NiC, not in COG; O, posttranslational modification, protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking, secretion, vesicular transport; V, defense mechanisms; W, extracellular structures; X, mobilome: prophages, transposons; Y, nuclear structure; Z, cytoskeleton. Mapping to Dn. limcola versus Dn. magnum and protein prediction versus identification is indicated in the insert. Underlying data are compiled in online suppl. Table S1b PCA plots considering the portion of proteins detected of the genomic potential per COG category for Dn. limicola (top), Dn. magnum (center), and both strains combined (bottom). Abbreviations (in alphabetic order): But, butyrate; Bz, benzoate; p -Cre, p -cresol; Lac, lactate; FA-Mix, fatty acid mixture; Fum, fumarate; Mal, malate; 4OHBz, 4-hydroxybenzoate; Phac, phenylacetate; 3-Ppp, 3-phenylpropionate; Prop, propionate; PropOH, propanol; Suc, succinate. c Proteomic coverage and genomic share across major modules of the catabolic network (see Fig. 3) comparing the two Desulfonema strains.

Fig. 3

Gene organisation in Dn. limicola (Dnl) and Dn. magnum (Dnm) with respect to anaerobic degradation of aromatic (a) and aliphatic (b) compounds (numbering as in Fig. 1) and to energy metabolism (c). Color coding of genes according to functional groups is indicated in the insert. Gray and white boxes below the genes denote gene products that have been identified or predicted only, respectively. Predicted functions of gene products and underlying proteomic data are compiled in online suppl. Tables S2 and S3. Homologous gene clusters are indicated by gray wedges.

Fig. 4

Composite catabolic network of Dn. limicola and Dn. magnum. Assignment of protein constituents to the two Desulfonema strains and the state of identification is indicated in the insert. Putative electron flow is indicated by dashed lines. Proteins marked with stars (*) are present as paralogs in the respective organism. Compound numbering and names are as detailed in the legend to Fig. 1. Predicted functions of gene products and underlying proteomic data are compiled in online suppl. Tables S2 and S3.

Fig. 5

Heat-map representation of substrate-specific proteome profiles of Dn. limicola and Dn. magnum. Growth substrates analyzed in both organisms are highlighted in bold. Compound numbering is as in Fig. 1. Scale of meta scores underlying protein identification is shown at the bottom. Absence of paralogue is indicated in gray. Proteins are sorted as indicated by color-coded grouping (left). Abbreviations are as detailed in the legend to Fig. 2.