hypDas a Marker for [NiFe]-Hydrogenases in Microbial Communities of Surface Waters

ABSTRACTHydrogen is an important trace gas in the atmosphere. Soil microorganisms are known to be an important part of the biogeochemical H2cycle, contributing 80 to 90% of the annual hydrogen uptake. Different aquatic ecosystems act as either sources or sinks of hydrogen, but the contribution of their microbial communities is unknown. [NiFe]-hydrogenases are the best candidates for hydrogen turnover in these environments since they are able to cope with oxygen. As they lack sufficiently conserved sequence motifs, reliable markers for these enzymes are missing, and consequently, little is known about their environmental distribution. We analyzed the essential maturation genes of [NiFe]-hydrogenases, including their frequency of horizontal gene transfer, and foundhypDto be an applicable marker for the detection of the different known hydrogenase groups. Investigation of two freshwater lakes showed that [NiFe]-hydrogenases occur in many prokaryotic orders. We found that the respectivehypDgenes cooccur with oxygen-tolerant [NiFe]-hydrogenases (groups 1 and 5) mainly ofActinobacteria,Acidobacteria, andBurkholderiales; cyanobacterial uptake hydrogenases (group 2a) of cyanobacteria; H2-sensing hydrogenases (group 2b) ofBurkholderiales,Rhizobiales, andRhodobacterales; and two groups of multimeric soluble hydrogenases (groups 3b and 3d) ofLegionellalesand cyanobacteria. These findings support and expand a previous analysis of metagenomic data (M. Barz et al., PLoS One 5:e13846, 2010,http://dx.doi.org/10.1371/journal.pone.0013846) and further identify [NiFe]-hydrogenases that could be involved in hydrogen cycling in aquatic surface waters.

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Conserved sequence motifs among bacterial, eukaryotic, and archaeal phosphatases that define a new phosphohydrolase superfamily

Protein Science ◽

10.1002/pro.5560070722 ◽

1998 ◽

Vol 7 (7) ◽

pp. 1647-1652 ◽

Cited By ~ 96

Author(s):

Maria Cristina Thaller ◽

Serena Schippa ◽

Gian Maria Rossolini

Keyword(s):

Sequence Motifs ◽

Conserved Sequence ◽

Conserved Sequence Motifs

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Identification and Analysis of Novel Amino-Acid Sequence Repeats inBacillus anthracisstr.AmesProteome Using Computational Tools

Comparative and Functional Genomics ◽

10.1155/2007/47161 ◽

2007 ◽

Vol 2007 ◽

pp. 1-23 ◽

Cited By ~ 2

Author(s):

G. R. Hemalatha ◽

D. Satyanarayana Rao ◽

L. Guruprasad

Keyword(s):

Amino Acid ◽

Amino Acid Residue ◽

Protein Sequence ◽

Amino Acid Residues ◽

Sequence Motifs ◽

Computational Tools ◽

Conserved Sequence ◽

Conserved Sequence Motifs ◽

Multiple Copies ◽

Domain 3

We have identified four repeats and ten domains that are novel in proteins encoded by theBacillus anthracisstr.Amesproteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1) 57-amino-acid-residue PxV domain, (2) 122-amino-acid-residue FxF domain, (3) 111-amino-acid-residue YEFF domain, (4) 109-amino-acid-residue IMxxH domain, (5) 103-amino-acid-residue VxxT domain, (6) 84-amino-acid-residue ExW domain, (7) 104-amino-acid-residue NTGFIG domain, (8) 36-amino-acid-residue NxGK repeat, (9) 95-amino-acid-residue VYV domain, (10) 75-amino-acid-residue KEWE domain, (11) 59-amino-acid-residue AFL domain, (12) 53-amino-acid-residue RIDVK repeat, (13) (a) 41-amino-acid-residue AGQF repeat and (b) 42-amino-acid-residue GSAL repeat. A repeat or domain type is characterized by specific conserved sequence motifs. We discuss the presence of these repeats and domains in proteins from other genomes and their probable secondary structure.

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Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA

Molecular Biology and Evolution ◽

10.1093/oxfordjournals.molbev.a025552 ◽

1996 ◽

Vol 13 (1) ◽

pp. 150-169 ◽

Cited By ~ 181

Author(s):

R. E. Hickson ◽

C. Simon ◽

A. Cooper ◽

G. S. Spicer ◽

J. Sullivan ◽

...

Keyword(s):

Secondary Structure ◽

12S Rrna ◽

Sequence Motifs ◽

Conserved Sequence ◽

The Third ◽

Conserved Sequence Motifs

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Oral Spirochetes Implicated in Dental Diseases Are Widespread in Normal Human Subjects and Carry Extremely Diverse Integron Gene Cassettes

Applied and Environmental Microbiology ◽

10.1128/aem.00564-12 ◽

2012 ◽

Vol 78 (15) ◽

pp. 5288-5296 ◽

Cited By ~ 17

Author(s):

Yu-Wei Wu ◽

Mina Rho ◽

Thomas G. Doak ◽

Yuzhen Ye

Keyword(s):

Microbial Communities ◽

De Novo ◽

Human Subjects ◽

Human Microbiome ◽

Metagenomic Data ◽

De Bruijn Graph ◽

Content Type ◽

Gene Cassettes ◽

Dental Diseases ◽

Normal Human

ABSTRACTThe NIH Human Microbiome Project (HMP) has produced several hundred metagenomic data sets, allowing studies of the many functional elements in human-associated microbial communities. Here, we survey the distribution of oral spirochetes implicated in dental diseases in normal human individuals, using recombination sites associated with the chromosomal integron inTreponemagenomes, taking advantage of the multiple copies of the integron recombination sites (repeats) in the genomes, and using a targeted assembly approach that we have developed. We find that integron-containingTreponemaspecies are present in ∼80% of the normal human subjects included in the HMP. Further, we are able tode novoassemble the integron gene cassettes using our constrained assembly approach, which employs a unique application of the de Bruijn graph assembly information; most of these cassette genes were not assembled in whole-metagenome assemblies and could not be identified by mapping sequencing reads onto the known referenceTreponemagenomes due to the dynamic nature of integron gene cassettes. Our study significantly enriches the gene pool known to be carried byTreponemachromosomal integrons, totaling 826 (598 97% nonredundant) genes. We characterize the functions of these gene cassettes: many of these genes have unknown functions. The integron gene cassette arrays found in the human microbiome are extraordinarily dynamic, with different microbial communities sharing only a small number of common genes.

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SAND, a New Protein Family: From Nucleic Acid to Protein Structure and Function Prediction

Comparative and Functional Genomics ◽

10.1002/cfg.93 ◽

2001 ◽

Vol 2 (4) ◽

pp. 226-235 ◽

Cited By ~ 5

Author(s):

Amanda Cottage ◽

Yvonne J. K. Edwards ◽

Greg Elgar

Keyword(s):

Genomic Sequence ◽

Protein Family ◽

Sequence Motifs ◽

Est Database ◽

Computational Tools ◽

Conserved Sequence ◽

Conserved Sequence Motifs ◽

And Function ◽

New Protein ◽

Genomic Organisation

As a result of genome, EST and cDNA sequencing projects, there are huge numbers of predicted and/or partially characterised protein sequences compared with a relatively small number of proteins with experimentally determined function and structure. Thus, there is a considerable attention focused on the accurate prediction of gene function and structure from sequence by using bioinformatics. In the course of our analysis of genomic sequence fromFugu rubripes, we identified a novel gene,SAND, with significant sequence identity to hypothetical proteins predicted inSaccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, aDrosophila melanogastergene, and mouse and human cDNAs. Here we identify a furtherSANDhomologue in human andArabidopsis thalianaby use of standard computational tools. We describe the genomic organisation ofSANDin these evolutionarily divergent species and identify sequence homologues from EST database searches confirming the expression of SAND in over 20 different eukaryotes. We confirm the expression of two different SAND paralogues in mammals and determine expression of one SAND in other vertebrates and eukaryotes. Furthermore, we predict structural properties of SAND, and characterise conserved sequence motifs in this protein family.

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