A trimodular family 16 glycoside hydrolase from the cellulosome of Ruminococcus flavefaciens displays highly specific licheninase (EC 3.2.1.73) activity

Microbiology ◽  
2021 ◽  
Vol 167 (7) ◽  
Author(s):  
Sunetra Mondal ◽  
Abhijeet Thakur ◽  
Carlos M. G. A. Fontes ◽  
Arun Goyal
Keyword(s):  
Glycoside Hydrolase ◽  
Type Species ◽  
Catalytic Mechanism ◽  
Biochemical Characterization ◽  
Maximum Activity ◽  
Significant Activity ◽  
Ruminococcus Flavefaciens ◽  
Content Type ◽  
Catalytic Domains ◽  
Link Type

Cellulosomes are highly complex cell-bound multi-enzymatic nanomachines used by anaerobes to break down plant carbohydrates. The genome sequence of Ruminococcus flavefaciens revealed a remarkably diverse cellulosome composed of more than 200 cellulosomal enzymes. Here we provide a detailed biochemical characterization of a highly elaborate R. flavefaciens cellulosomal enzyme containing an N-terminal dockerin module, which anchors the enzyme into the multi-enzyme complex through binding of cohesins located in non-catalytic cell-bound scaffoldins, and three tandemly repeated family 16 glycoside hydrolase (GH16) catalytic domains. The DNA sequence encoding the three homologous catalytic domains was cloned and hyper-expressed in Escherichia coli BL21 (DE3) cells. SDS-PAGE analysis of purified His6 tag containing RfGH16_21 showed a single soluble protein of molecular size ~89 kDa, which was in agreement with the theoretical size, 89.3 kDa. The enzyme RfGH16_21 exhibited activity over a wide pH range (pH 5.0–8.0) and a broad temperature range (50–70 °C), displaying maximum activity at an optimum pH of 7.0 and optimum temperature of 55 °C. Substrate specificity analysis of RfGH16_21 revealed maximum activity against barley β-d-glucan (257 U mg−1) followed by lichenan (247 U mg−1), but did not show significant activity towards other tested polysaccharides, suggesting that it is specifically a β-1,3-1,4-endoglucanase. TLC analysis revealed that RfGH16_21 hydrolyses barley β-d-glucan to cellotriose, cellotetraose and a higher degree of polymerization of gluco-oligosaccharides indicating an endo-acting catalytic mechanism. This study revealed a fairly high, active and thermostable bacterial endo-glucanase which may find considerable biotechnological potentials.

Flavobacterium cutihirudinis sp. nov., isolated from the skin of the medical leech Hirudo verbana

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2841-2847 ◽  
Author(s):  
S. P. Glaeser ◽  
H. Galatis ◽  
K. Martin ◽  
P. Kämpfer
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Biochemical Characterization ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Hirudo Verbana

A Gram-staining-negative, non-endospore-forming, yellow-pigmented strain (E89T) was isolated from the skin of the medical leech Hirudo verbana obtained from a leech farm located in Biebertal, Germany. 16S rRNA gene sequencing analysis showed that the isolate was grouped in the genus Flavobacterium . Strain E89T was most closely related to Flavobacterium chilense LM-09-FpT (98.2 %), Flavobacterium chungangense CJ7T (98.1 %), and Flavobacterium oncorhynchi 631-08T (98.1 %). 16S rRNA gene sequence similarities to all other species of the genus Flavobacterium were ≤97.4 %. A menaquinone of the type MK-6 was found to be the predominant respiratory quinone and the polar lipid profile consisted of the major compounds phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids, one unknown phospholipid and two unknown lipids. The fatty acid profile was composed of iso-C15 : 0, C15 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) found in major amounts and several hydroxylated fatty acids in smaller amounts, among them iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. All these data support the allocation of the isolate in the genus Flavobacterium . Physiological/biochemical characterization and DNA–DNA hybridizations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of the strain. Based on these data, strain E89T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium cutihirudinis sp. nov. is proposed. The type strain is E89T ( = DSM 25795T = LMG 26922T = CIP 110374T).

scholarly journals Re-examination of the taxonomic status of Enterobacter helveticus, Enterobacter pulveris and Enterobacter turicensis as members of the genus Cronobacter and their reclassification in the genera Franconibacter gen. nov. and Siccibacter gen. nov. as Franconibacter helveticus comb. nov., Franconibacter pulveris comb. nov. and Siccibacter turicensis comb. nov., respectively

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3402-3410 ◽  
Author(s):  
Roger Stephan ◽  
Christopher J. Grim ◽  
Gopal R. Gopinath ◽  
Mark K. Mammel ◽  
Venugopal Sathyamoorthy ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Biochemical Characterization ◽  
Novel Species ◽  
Taxonomic Status ◽  
New Genera ◽  
Content Type ◽  
Link Type ◽  
Genome Scale

Recently, a taxonomical re-evaluation of the genus Enterobacter , based on multi-locus sequence typing (MLST) analysis, has led to the proposal that the species Enterobacter pulveris , Enterobacter helveticus and Enterobacter turicensis should be reclassified as novel species of the genus Cronobacter . In the present work, new genome-scale analyses, including average nucleotide identity, genome-scale phylogeny and k-mer analysis, coupled with previously reported DNA–DNA hybridization values and biochemical characterization strongly indicate that these three species of the genus Enterobacter are not members of the genus Cronobacter , nor do they belong to the re-evaluated genus Enterobacter . Furthermore, data from this polyphasic study indicated that all three species constitute two new genera. We propose reclassifying Enterobacter pulveris and Enterobacter helveticus in the genus Franconibacter gen. nov. as Franconibacter pulveris comb. nov. (type strain 601/05T = LMG 24057T = DSM 19144T) and Franconibacter helveticus comb. nov. (type strain 513/05T = LMG 23732T = DSM 18396T), respectively, and Enterobacter turicensis in the genus Siccibacter gen. nov. as Siccibacter turicensis comb. nov. (type strain 508/05T = LMG 23730T = DSM 18397T).

scholarly journals Methylobacterium cerastii sp. nov., isolated from the leaf surface of Cerastium holosteoides

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 917-924 ◽  
Author(s):  
S. Wellner ◽  
N. Lodders ◽  
P. Kämpfer
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Biochemical Characterization ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two Gram-stain-negative, non-endospore-forming, rod-like strains, designated C15T and C44, were isolated from the phyllosphere of Cerastium holosteoides and were studied in detail in order to assess their taxonomic position. 16S rRNA gene sequence analysis allocated both isolates clearly to the genus Methylobacterium . Both strains showed the highest 16S rRNA gene sequence similarity to Methylobacterium marchantiae JT1T (97.5 %) and Methylobacterium jeotgali S2R03-9T (97.4 %). The fatty acid profiles contained major amounts of C16 : 0, C18 : 1ω7c and C16 : 1ω7c/iso-C15 : 0 2-OH (summed feature 3), which supported the grouping of the isolates in the genus Methylobacterium . Physiological/biochemical characterization and DNA–DNA hybridizations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of the strains. For this reason, we propose for strain C15T ( = DSM 23679T  = CCUG 60040T  = CCM 7788T) a novel species with the name Methylobacterium cerastii sp. nov. Strain C44 ( = DSM 23675  = CCM 7789) is an additional strain of M. cerastii.

Rhodococcus defluvii sp. nov., isolated from wastewater of a bioreactor and formal proposal to reclassify [Corynebacterium hoagii] and Rhodococcus equi as Rhodococcus hoagii comb. nov.

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 755-761 ◽  
Author(s):  
P. Kämpfer ◽  
W. Dott ◽  
K. Martin ◽  
S. P. Glaeser
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Biochemical Characterization ◽  
Sequence Similarity ◽  
Rhodococcus Equi ◽  
Rhodococcus Opacus ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-positive, non-endospore-forming rod-shaped bacterium, strain Ca11T, was isolated from a bioreactor with extensive phosphorus removal and was studied in detail for its taxonomic allocation. 16S rRNA gene sequence analysis revealed closest sequence similarity of the strain to type strains of [ Corynebacterium hoagii ] and Rhodococcus equi (98.9 %), Rhodococcus koreensis and Rhodococcus wratislaviensis (both 98.4 %), Rhodococcus opacus and Rhodococcus canchipurensis (both 98.0 %) followed by Rhodococcus kunmingensis and Rhodococcus imtechensis (97.7 %). Phylogenetic trees showed a distinct clustering of strain Ca11T with the type strains of [ C. hoagii ], R. equi , and R. kunmingensis separate to all other species of the genus Rhodococcus . The quinone system of strain Ca11T was composed of dihydrogenated menaquinones with 8 (major amount) as well as 7 and 6 isoprenoid units [MK-8(H2), MK-7(H2), MK-6(H2)]. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, one unknown phospholipid and an unidentified glycolipid. The fatty acid profile was similar to that reported for R. equi and contained major amounts of C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0, supporting the allocation of the strain to the genus Rhodococcus . Physiological and biochemical characterization and DNA–DNA hybridization with type strains of the most closely related species allowed clear phenotypic and genotypic differentiation of the isolate. On the basis of these results, strain Ca11T ( = DSM 45893T = LMG 27563T) represents a novel species of the genus Rhodococcus , with the proposed name Rhodococcus defluvii sp. nov. In addition, a polyphasic taxonomic analysis of [ Corynebacterium hoagii ] DSM 20295T and Rhodococcus equi DSM 20307T indicated that the two strains belong to the same species, for which the name Rhodococcus hoagii comb. nov. takes priority, according to the Rules of the Bacteriological Code.

Martelella endophytica sp. nov., an antifungal bacterium associated with a halophyte

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2914-2919 ◽  
Author(s):  
Fehmida Bibi ◽  
Eu Jin Chung ◽  
Ajmal Khan ◽  
Che Ok Jeon ◽  
Young Ryun Chung
Keyword(s):  
Type Species ◽  
Plant Pathogens ◽  
Biochemical Characterization ◽  
Endophytic Bacterium ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Hybridization Data ◽  
Gram Staining

A Gram-staining-negative, non-spore-forming endophytic bacterium, designated strain YC6887T, was isolated from a root sample of a halophyte, Rosa rugosa, collected from a tidal flat area of Namhae Island, located at the southern end of Korea. Strain YC6887T was found to exhibit inhibitory activity against oomycete plant pathogens. The cells were non-motile and aerobic rods. The strain was able to grow at 4–40 °C (optimum 28–30 °C) and at pH 5.0–9.0 (optimum pH 7.0–8.5). Strain YC6887T was able to grow at NaCl concentrations of 0–9 % (w/v) with optimum growth at 4–5 % (w/v) NaCl, but NaCl is not essential for growth. Comparison of 16S rRNA gene sequences showed that the strain was a member of the genus Martelella , a member of order Rhizobiales , exhibiting highest similarity with Martelella mediterranea (98.6 %). The DNA–DNA relatedness between strain YC6887T and M. mediterranea MACL11T was 19.8±6.8. Chemotaxonomically, strain YC6887T contained C19 : 0 cyclo ω8c (28.0 %) and C18 : 1ω7c (17.9 %) as predominant fatty acids, confirming the affiliation of strain YC6887T with the genus Martelella . The major respiratory quinone was Q-10 and the DNA G+C content was 62.1 mol%. On the basis of phylogenetic analysis, physiological and biochemical characterization and DNA–DNA hybridization data, strain YC6887T should be classified as representing a novel species of the genus Martelella , for which the name Martelella endophytica sp. nov. is proposed. The type strain is YC6887T ( = KCCM 43011T = NBRC 109149T).

scholarly journals Lactobacillus porcinae sp. nov., isolated from traditional Vietnamese nem chua

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1754-1759 ◽  
Author(s):  
Doan Thi Lam Nguyen ◽  
Margo Cnockaert ◽  
Koenraad Van Hoorde ◽  
Evie De Brandt ◽  
Isabel Snauwaert ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Biochemical Characterization ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Fermentation Profile

A species diversity study of lactic acid bacteria occurring in traditional Vietnamese nem chua yielded an isolate, LMG 26767T, that could not be assigned to a species with a validly published name. The isolate was initially investigated by 16S rRNA gene sequence analysis, which revealed that it belonged to the genus Lactobacillus , with Lactobacillus manihotivorans and Lactobacillus camelliae as the closest relatives (98.9 % and 96.9 % gene sequence similarity to the type strains, respectively). Comparative (GTG)5-PCR genomic fingerprinting confirmed the unique taxonomic status of the novel strain. DNA–DNA hybridization experiments, DNA G+C content determination, sequence analysis of the phenylalanyl-tRNA synthase (pheS) gene, and physiological and biochemical characterization demonstrated that strain LMG 26767T represents a novel species, for which the name Lactobacillus porcinae sp. nov. is proposed; the type strain is LMG 26767T ( = CCUG 62266T). Biochemically, L. porcinae can be distinguished from L. manihotivorans and L. camelliae by its carbohydrate fermentation profile, absence of growth at 45 °C, and production of d- and l-lactate as end products of glucose metabolism.

scholarly journals Reclassification of Staphylococcus jettensis De Bel et al. 2013 as Staphylococcus petrasii subsp. jettensis subsp. nov. and emended description of Staphylococcus petrasii Pantucek et al. 2013

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4198-4201 ◽  
Author(s):  
Annelies De Bel ◽  
Pavel Švec ◽  
Petr Petráš ◽  
Ivo Sedláček ◽  
Roman Pantůček ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Repetitive Sequence ◽  
Type Strain ◽  
Type Species ◽  
Biochemical Characterization ◽  
Species Description ◽  
Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Emended Description

The type and clinical strains of two recently described coagulase-negative species of the genus Staphylococcus, Staphylococcus petrasii and Staphylococcus jettensis , were compared using dnaJ, tuf, gap, hsp60 and rpoB gene sequences, DNA–DNA hybridization, ribotyping, repetitive sequence-based PCR fingerprinting and extensive biochemical characterization. Based on the results, the species description of S. petrasii has been emended and S. jettensis should be reclassified as a novel subspecies within S. petrasii for which the name Staphylococcus petrasii subsp. jettensis subsp. nov. is proposed. The type strain is SEQ110T ( = LMG 26879T = CCUG 62657T = DSM 26618T = CCM 8494T).

scholarly journals Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.

scholarly journals Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).

Litorilinea aerophila gen. nov., sp. nov., an aerobic member of the class Caldilineae , phylum Chloroflexi , isolated from an intertidal hot spring

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1149-1154 ◽  
Author(s):  
Varsha Kale ◽  
Snædís H. Björnsdóttir ◽  
Ólafur H. Friðjónsson ◽  
Sólveig K. Pétursdóttir ◽  
Sesselja Ómarsdóttir ◽  
...  
Keyword(s):  
Type Species ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Phenotypic Differences ◽  
Link Type ◽  
Fermentative Growth ◽  
Distinct Lineage ◽  
Ph Range

A thermophilic, aerobic, Gram-stain-negative, filamentous bacterium, strain PRI-4131T, was isolated from an intertidal hot spring in Isafjardardjup, NW Iceland. The strain grew chemo-organotrophically on various carbohydrates. The temperature range for growth was 40–65 °C (optimum 55 °C), the pH range was pH 6.5–9.0 (optimum pH 7.0) and the NaCl range was 0–3 % (w/v) (optimum 0.5 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PRI-4131T represented a distinct lineage within the class Caldilineae of the phylum Chloroflexi. The highest levels of sequence similarity, about 91 %, were with Caldilinea aerophila STL-6-O1T and Caldilinea tarbellica D1-25-10-4T. Fermentative growth was not observed for strain PRI-4131T, which, in addition to other characteristics, distinguished it from the two Caldilinea species. Owing to both phylogenetic and phenotypic differences from the described members of the class Caldilineae , we propose to accommodate strain PRI-4131T in a novel species in a new genus, Litorilinea aerophila gen. nov., sp. nov. The type strain of Litorilinea aerophila is PRI-4131T ( = DSM 25763T  = ATCC BAA-2444T).

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