High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1^T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism

Strain JKG1^T was isolated from a cellulolytic enrichment in Great Boiling Spring, Nevada (1), using optical tweezers and a microfluidic device due to its capacity to grow aerobically on filter paper (optimum 55 °C) (2). Strain JKG1^T was described as a member of a new genus and species, Kallotenue papyrolyticum, and a new order, Kallotenuales, of the phylum Chloroflexi (2). It has broad heterotrophic activity, including the capacity to hydrolyze polysaccharides such as carboxymethylcellulose, microcrystalline cellulose, filter paper, xylan, and starch, and proteinaceous substrates such as casamino acids, tryptone, and peptone. K. papyrolyticum is one of several, new high-level taxonomic groups of thermophilic Chloroflexi isolated from Great Boiling spring (3).

The draft genome of strain JKG1^T was generated at the DOE Joint genome Institute (JGI) using Pacific Biosciences (PacBio) technology. A PacBio SMRTbell library was constructed and sequenced on the PacBio RS platform, which generated 304,235 filtered subreads totaling 854.0 Mbp. All general aspects of library construction and sequencing performed at the JGI can be found at http://www.jgi.doe.gov. The raw reads were assembled using HGAP (version 2.0.0) (4). The genome was annotated using Prodigal version 2.5 (5), as part of the JGI microbial annotation pipeline (6). The K. papyrolyticum draft genome is 4,475,263 bp in 4 contigs, encoding 4,010 predicted genes, including 49 tRNA-encoding genes, and three rRNA operons. The genome encodes enzymes for complete glycolysis, tricarboxylic acid cycle, and pentose phosphate pathways and dedicates a large amount of its genome to carbohydrate (10.1%; clusters of orthologous groups [COG] category G) and amino acid (8.9%; COG category E) metabolism. Analysis of the genome for carbohydrate-active enzymes (CAZymes) (7) revealed 171 total CAZymes, 55 of which are glycoside hydrolases (GHs), including GHs putatively involved in chitin (GH18), woody plant (GH53), and cellulose (GH5,6,9,10,51) depolymerization. This number of CAZymes and GH domains is similar to other cellulolytic thermophiles, such as Thermotoga maritima (8), Caldicellulosiruptor species (9), and Dictyoglomus turgidum (10).

Catabolism of organic compounds can be coupled to aerobic respiration. Similar to Chloroflexus (11), strain JKG1^T has a prototypical respiratory complex I and II to transfer electrons into the quinone pool; however, quinols are likely oxidized by an alternative complex III (ACIII) (12) rather than a bc₁/b₆f complex The presence of lactate and ethanol dehydrogenases, acetate-CoA ligase, and an iron-only hydrogenase suggest capacity for fermentation, however, fermentation of glucose, casamino acids, or yeast extract was not observed in JKG1^T cultures (2). Strain JKG1^T may be able to oxidize carbon monoxide through a putative type II carbon monoxide dehydrogenase (CODH) encoded by a cox gene cluster, although the functions of type II CODH are not firmly established (13). Known pathways for phototrophy, autotrophy, and anaerobic respiration are absent, although putative molybdopterin oxidoreductases and multicopper oxidases may be involved in anaerobic respiration.

PFAM domains representing proteins involved in outer membrane biogenesis and transport are not present, suggesting JKG1^T has a monoderm cell envelope structure similar to other Chloroflexi (14).

The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-05CH11231. Additional support was supported by NSF grant OISE-0968421 to B.P.H. who is also grateful for support from Greg Fullmer through the UNLV Foundation.