Analysis of the complete genome sequence of the archaeon Pyrococcus chitonophagus DSM 10152 (formerly Thermococcus chitonophagus)

Papadimitriou, Konstantinos; Baharidis, Panagiotis K.; Georgoulis, Anastasios D.; Engel, Marion; Louka, Maria; Karamolegkou, Georgia; Tsoka, Aggeliki; Blom, Jochen; Pot, Bruno; Malecki, P.; Rypniewski, W.; Huber, Harald; Schloter, Michael; Vorgias, Constantinos E.

doi:10.1007/s00792-016-0826-x

Cited by 7 publications

(5 citation statements)

References 51 publications

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“…Multiple samples of spider exoskeleton, including fragments of cuticle and setae, were incubated with four chitinases: Chi60 from M. marina and its deletion mutant, missing two Ig-like domains [101] and two chitinases, Chiton_1119 and Chiton_1716, from P. chitonophagus [102]. The samples were incubated with the enzymes at 18, 28, and subsequently 35 °C, for at least 48 h at each temperature.…”

Section: Methodsmentioning

confidence: 99%

Spider Chitin: An Ultrafast Microwave-Assisted Method for Chitin Isolation from Caribena versicolor Spider Molt Cuticle

et al. 2019

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Chitin, as a fundamental polysaccharide in invertebrate skeletons, continues to be actively investigated, especially with respect to new sources and the development of effective methods for its extraction. Recent attention has been focused on marine crustaceans and sponges; however, the potential of spiders (order Araneae) as an alternative source of tubular chitin has been overlooked. In this work, we focused our attention on chitin from up to 12 cm-large Theraphosidae spiders, popularly known as tarantulas or bird-eating spiders. These organisms “lose” large quantities of cuticles during their molting cycle. Here, we present for the first time a highly effective method for the isolation of chitin from Caribena versicolor spider molt cuticle, as well as its identification and characterization using modern analytical methods. We suggest that the tube-like molt cuticle of this spider can serve as a naturally prefabricated and renewable source of tubular chitin with high potential for application in technology and biomedicine.

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Section: Methodsmentioning

confidence: 99%

Spider Chitin: An Ultrafast Microwave-Assisted Method for Chitin Isolation from Caribena versicolor Spider Molt Cuticle

et al. 2019

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“…chitonophagus is known to possess multiple chitinases (40)(41)(42). Recently, two groups of investigators have conducted genome analyses of this archaeon, and both predicted the presence of three chitinase genes (43,44). Reclassification of the organism to the genus Pyrococcus has also been proposed (species name Pyrococcus chitonophagus) (43).…”

Section: Discussionmentioning

confidence: 99%

“…Recently, two groups of investigators have conducted genome analyses of this archaeon, and both predicted the presence of three chitinase genes (43,44). Reclassification of the organism to the genus Pyrococcus has also been proposed (species name Pyrococcus chitonophagus) (43). Biochemical characterization of one of the T. chitonophagus chitinases, ChiD, has revealed that the enzyme is a structurally novel chitinase exhibiting exo-type activities and mainly releases (GlcNAc) 2 units from the reducing ends of chitin chains (44).…”

Section: Discussionmentioning

confidence: 99%

Engineering of the Hyperthermophilic Archaeon Thermococcus kodakarensis for Chitin-Dependent Hydrogen Production

Aslam

Horiuchi

Simons

et al. 2017

Appl Environ Microbiol

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Thermococcus kodakarensis is a hyperthermophilic archaeon that harbors a complete set of genes for chitin degradation to fructose 6-phosphate. However, wild-type T. kodakarensis KOD1 does not display growth on chitin. In this study, we developed a T. kodakarensis strain that can grow on chitin via genetic and adaptive engineering. First, a chitinase overproduction strain (KC01) was constructed by replacing the chitinase gene promoter with a strong promoter from the cell surface glycoprotein gene, resulting in increased degradation of swollen chitin and accumulation of N-,N=-diacetylchitobiose in the medium. To enhance N-,N=-diacetylchitobiose assimilation in KC01, genes encoding diacetylchitobiose deacetylase, exo-␤-D-glucosaminidase, and glucosamine-6-phosphate deaminase were also overexpressed to obtain strain KC04. To strengthen the glycolytic flux of KC04, the gene encoding Tgr (transcriptional repressor of glycolytic genes) was disrupted to obtain strain KC04Δt. In both KC04 and KC04Δt strains, degradation of swollen chitin was further enhanced. In the culture broth of these strains, the accumulation of glucosamine was observed. KC04Δt was repeatedly inoculated in a swollen-chitin-containing medium for 13 cultures. This adaptive engineering strategy resulted in the isolation of a strain (KC04ΔtM1) that showed almost complete degradation of 0.4% (wt/vol) swollen chitin after 90 h. The strain produced high levels of acetate and ammonium in the culture medium, and, moreover, molecular hydrogen was generated. This strongly suggests that strain KC04ΔtM1 has acquired the ability to convert chitin to fructose 6-phosphate via deacetylation and deamination and further convert fructose 6-phosphate to acetate via glycolysis coupled to hydrogen generation. IMPORTANCE Chitin is a linear homopolymer of ␤-1,4-linked N-acetylglucosamine and is the second most abundant biomass next to cellulose. Compared to the wealth of research focused on the microbial degradation and conversion of cellulose, studies addressing microbial chitin utilization are still limited. In this study, using the hyperthermophilic archaeon Thermococcus kodakarensis as a host, we have constructed a strain that displays chitin-dependent hydrogen generation. The apparent hydrogen yield per unit of sugar consumed was slightly higher with swollen chitin than with starch. As gene manipulation in T. kodakarensis is relatively simple, the strain constructed in this study can also be used as a parent strain for the development and expansion of chitin-dependent biorefinery, in addition to its capacity to produce hydrogen.

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“…All gene clusters related to chitin utilization are absent in Pa. pacificus, different to Pyrococcus and Thermococcus, such as P. furious [22], P. chitonophagus [23] and T. kodakaraensis KOD [24]. The lipolytic growth of T. sibiricus appears to be unique in the order Thermococcales [20].…”

Section: Utilization Of Carbohydratesmentioning

confidence: 99%

Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus pacificus DY20341T from Deep-Sea Hydrothermal Sediments

Zeng

Zhang

Shao

2020

IJMS

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The hyperthermo-piezophilic archaeon Palaeococcus pacificus DY20341T, isolated from East Pacific hydrothermal sediments, can utilize elemental sulfur as a terminal acceptor to simulate growth. To gain insight into sulfur metabolism, we performed a genomic and transcriptional analysis of Pa. pacificus DY20341T with/without elemental sulfur as an electron acceptor. In the 2001 protein-coding sequences of the genome, transcriptomic analysis showed that 108 genes increased (by up to 75.1 fold) and 336 genes decreased (by up to 13.9 fold) in the presence of elemental sulfur. Palaeococcus pacificus cultured with elemental sulfur promoted the following: the induction of membrane-bound hydrogenase (MBX), NADH:polysulfide oxidoreductase (NPSOR), NAD(P)H sulfur oxidoreductase (Nsr), sulfide dehydrogenase (SuDH), connected to the sulfur-reducing process, the upregulation of iron and nickel/cobalt transfer, iron–sulfur cluster-carrying proteins (NBP35), and some iron–sulfur cluster-containing proteins (SipA, SAM, CobQ, etc.). The accumulation of metal ions might further impact on regulators, e.g., SurR and TrmB. For growth in proteinous media without elemental sulfur, cells promoted flagelin, peptide/amino acids transporters, and maltose/sugar transporters to upregulate protein and starch/sugar utilization processes and riboflavin and thiamin biosynthesis. This indicates how strain DY20341T can adapt to different living conditions with/without elemental sulfur in the hydrothermal fields.

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Analysis of the complete genome sequence of the archaeon Pyrococcus chitonophagus DSM 10152 (formerly Thermococcus chitonophagus)

Cited by 7 publications

References 51 publications

Spider Chitin: An Ultrafast Microwave-Assisted Method for Chitin Isolation from Caribena versicolor Spider Molt Cuticle

Spider Chitin: An Ultrafast Microwave-Assisted Method for Chitin Isolation from Caribena versicolor Spider Molt Cuticle

Engineering of the Hyperthermophilic Archaeon Thermococcus kodakarensis for Chitin-Dependent Hydrogen Production

Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus pacificus DY20341T from Deep-Sea Hydrothermal Sediments

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