Diversity of Glycosyl Hydrolases from Cellulose-Depleting Communities Enriched from Casts of Two Earthworm Species

被引:53
作者
Beloqui, Ana [1 ]
Nechitaylo, Taras Y. [2 ]
Lopez-Cortes, Nieves [1 ]
Ghazi, Azam [1 ]
Guazzaroni, Maria-Eugenia [1 ]
Polaina, Julio [3 ]
Strittmatter, Axel W. [4 ]
Reva, Oleg [5 ]
Waliczek, Agnes [2 ]
Yakimov, Michail M. [6 ]
Golyshina, Olga V. [2 ,7 ]
Ferrer, Manuel [1 ]
Golyshin, Peter N. [2 ,7 ,8 ]
机构
[1] CSIC, Inst Catalysis, E-28049 Madrid, Spain
[2] HZI Helmholtz Ctr Infect Res, D-38124 Braunschweig, Germany
[3] CSIC, Inst Agroquim & Tecnol Alimentos, Valencia 46980, Spain
[4] Eurofins MWG Operon, D-85560 Ebersberg, Germany
[5] Univ Pretoria, Dept Biochem, ZA-0002 Pretoria, South Africa
[6] CNR, Ist Ambiente Marino Costiero, I-98122 Messina, Italy
[7] Bangor Univ, Sch Biol Sci, Bangor LL57 2UW, Gwynedd, Wales
[8] Aberystwyth Univ Bangor Univ Partnership, Ctr Integrated Res Rural Environm CRRE, Aberystwyth SY23 3BF, Ceredigion, Wales
关键词
CRYSTAL-STRUCTURE; APORRECTODEA-CALIGINOSA; SUBSTRATE-SPECIFICITY; LUMBRICUS-TERRESTRIS; FUNCTIONAL-ANALYSIS; GLYCOLYTIC-ENZYMES; BACTERIAL GENOMES; FAMILY; GUT; GENE;
D O I
10.1128/AEM.00902-10
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
The guts and casts of earthworms contain microbial assemblages that process large amounts of organic polymeric substrates from plant litter and soil; however, the enzymatic potential of these microbial communities remains largely unexplored. In the present work, we retrieved carbohydrate-modifying enzymes through the activity screening of metagenomic fosmid libraries from cellulose-depleting microbial communities established with the fresh casts of two earthworm species, Aporrectodea caliginosa and Lumbricus terrestris, as inocula. Eight glycosyl hydrolases (GHs) from the A. caliginosa-derived community were multidomain endo-beta-glucanases, beta-glucosidases, beta-cellobiohydrolases, beta-galactosidase, and beta-xylosidases of known GH families. In contrast, two GHs derived from the L. terrestris microbiome had no similarity to any known GHs and represented two novel families of beta-galactosidases/alpha -arabinopyranosidases. Members of these families were annotated in public databases as conserved hypothetical proteins, with one being structurally related to isomerases/dehydratases. This study provides insight into their biochemistry, domain structures, and active-site architecture. The two communities were similar in bacterial composition but significantly different with regard to their eukaryotic inhabitants. Further sequence analysis of fosmids and plasmids bearing the GH-encoding genes, along with oligonucleotide usage pattern analysis, suggested that those apparently originated from Gammaproteobacteria (pseudomonads and Cellvibrio-like organisms), Betaproteobacteria (Comamonadaceae), and Alphaproteobacteria (Rhizobiales).
引用
收藏
页码:5934 / 5946
页数:13
相关论文
共 77 条
[51]   GeneMark.hmm: new solutions for gene finding [J].
Lukashin, AV ;
Borodovsky, M .
NUCLEIC ACIDS RESEARCH, 1998, 26 (04) :1107-1115
[52]   Genomics - Gene duplication and evolution [J].
Lynch, M .
SCIENCE, 2002, 297 (5583) :945-947
[53]   Diversity and expression of nitrogen fixation genes in bacterial symbionts of marine sponges [J].
Mohamed, Naglaa M. ;
Colman, Albert S. ;
Tal, Yossi ;
Hill, Russell T. .
ENVIRONMENTAL MICROBIOLOGY, 2008, 10 (11) :2910-2921
[54]   Effect of the Earthworms Lumbricus terrestris and Aporrectodea caliginosa on Bacterial Diversity in Soil [J].
Nechitaylo, Taras Y. ;
Yakimov, Michail M. ;
Godinho, Miguel ;
Timmis, Kenneth N. ;
Belogolova, Elena ;
Byzov, Boris A. ;
Kurakov, Alexander V. ;
Jones, David L. ;
Golyshin, Peter N. .
MICROBIAL ECOLOGY, 2010, 59 (03) :574-587
[55]   'Candidatus Lumbricincola', a novel lineage of uncultured Mollicutes from earthworms of family Lumbricidae [J].
Nechitaylo, Taras Y. ;
Timmis, Kenneth N. ;
Golyshin, Peter N. .
ENVIRONMENTAL MICROBIOLOGY, 2009, 11 (04) :1016-1026
[56]   The contribution of endogenous cellulase to the cellulose digestion in the gut of earthworm (Pheretima hilgendorfi: Megascolecidae) [J].
Nozaki, Mana ;
Miura, Chiemi ;
Tozawa, Yuzuru ;
Miura, Takeshi .
SOIL BIOLOGY & BIOCHEMISTRY, 2009, 41 (04) :762-769
[57]   Diverse genes of cellulase homologues of glycosyl hydrolase family 45 from the symbiotic protists in the hindgut of the termite Reticulitermes speratus [J].
Ohtoko, K ;
Ohkuma, M ;
Moriya, S ;
Inoue, T ;
Usami, R ;
Kudo, T .
EXTREMOPHILES, 2000, 4 (06) :343-349
[58]   A MICROBIOLOGICAL STUDY OF EARTHWORM CASTS [J].
PARLE, JN .
JOURNAL OF GENERAL MICROBIOLOGY, 1963, 31 (01) :13-&
[59]   Differentiation of regions with atypical oligonucleotide composition in bacterial genomes -: art. no. 251 [J].
Reva, ON ;
Tümmler, B .
BMC BIOINFORMATICS, 2005, 6 (1)
[60]   Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns -: art. no. 90 [J].
Reva, ON ;
Tümmler, B .
BMC BIOINFORMATICS, 2004, 5 (1)