Comparative genomics reveals a deep-sea sediment-adapted life style of <i>Pseudoalteromonas</i> sp. SM9913

Qin, Qi‐Long; Li, Yang; Zhang, Yan-Jiao; Zhou, Zhemin; Zhang, Weixin; Chen, Xiu-Lan; Zhang, Xiying; Zhou, Biao; Wang, Lei; Zhang, Yuzhong

doi:10.1038/ismej.2010.103

Cited by 112 publications

(91 citation statements)

References 63 publications

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“…Third, virus-directed augmentation of motility is suggested by ACE POV-encoded pseudaminic synthase (pseI), which likely glycosylates flagellins (Hopf et al, 2011). Flagellar genes (flaB and motA) are critical for maintaining mobility and particle association for deep sea bacteria (Eloe et al, 2008;Qin et al, 2011). Such genes for 'chemotaxis and motility' have been observed previously in viromes (Dinsdale et al, 2008) and may boost their host's motility to improve nutrient acquisition in the deep sea.…”

Section: Co-localized With Viral Genes On Contigs (Includes Genes Idementioning

confidence: 99%

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

2014

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Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large-scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established ‘core’ (180 PCs; one-third new to science) and ‘flexible’ (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (<5% of PCs) and revealed depth-related taxonomic patterns. Functional annotation, coupled with extensive analyses to document non-viral DNA contamination, uncovered 32 new AMGs (9 core, 20 photic and 3 aphotic) that introduce ways in which viruses manipulate infected host metabolism, and parallel depth-stratified host adaptations (for example, photic zone genes for iron–sulphur cluster modulation for phage production, and aphotic zone genes for high-pressure deep-sea survival). Finally, significant vertical flux of photic zone viruses to the deep sea was detected, which is critical for interpreting depth-related patterns in nature. Beyond the ecological advances outlined here, this catalog of viral core, flexible and niche-defining genes provides a resource for future investigation into the organization, function and evolution of microbial molecular networks to mechanistically understand and model viral roles in the biosphere.

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Section: Co-localized With Viral Genes On Contigs (Includes Genes Idementioning

confidence: 99%

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

2014

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“…The genus contains specialists for various marine habitats ranging from sea ice (9) to deep-sea sediments (10). Its species are divided into pigmented and nonpigmented species; the former are known for habitation of marine biofilms and production of antimicrobial and algicidal substances, while the latter are found living dispersed in the water column (11).…”

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confidence: 99%

Morphology, Physiological Characteristics, and Complete Sequence of Marine Bacteriophage ϕRIO-1 Infecting Pseudoalteromonas marina

Hardies

Hwang

et al. 2013

J Virol

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c Bacteria of the genus Pseudoalteromonas are ubiquitous in the world's oceans. Marine bacteria have been posited to be associated with a major ancient branch of podoviruses related to T7. Yet, although Pseudoalteromonas phages belonging to the Corticoviridae and the Siphoviridae and prophages belonging to the Myoviridae have been reported, no Pseudoalteromonas podovirus was previously known. Here, a new lytic Pseudoalteromonas marina phage, RIO-1, belonging to the Podoviridae was isolated and characterized with respect to morphology, genomic sequence, and biological properties. Its major encoded proteins were distantly similar to those of T7. The most similar previously sequenced viruses were Pseudomonas phage PA11 and Salinivibrio phage CW02. Whereas many elements of the morphology and gene organization of RIO-1 are similar to those of podoviruses broadly related to T7, RIO-1 conspicuously lacked an RNA polymerase gene. Since definitions of a T7 supergroup have included similarity in the DNA polymerase gene, a detailed phylogenetic analysis was conducted, and two major DNA polymerase clades in Autographivirinae and several structural variants of the polA family represented in podoviruses were found. RIO-1 carries an operon similar to that in a few other podoviruses predicted to specify activities related to ␥-glutamyl amide linkages and/or unusual peptide bonds. Most growth properties of RIO-1 were typical of T7-like phages, except for a long latent period.V iral particles outnumber bacteria in the world's oceans by a factor of about 10:1 and are thought to enforce diversity at the base of the microbiological community by restraining overgrowth of any particularly successful microbial species and returning their biomolecules as nutrients into the water through lysis (1, 2). This role rests critically on a network of specific host-virus interactions. Estimates of viral diversity by metagenomics tend to indicate extraordinarily high numbers of viral species (3-5), yet the total number of sequenced marine bacteriophages as of the last published count (6) was only 17. Current marine phage sequencing initiatives are expected to raise this to only a few hundred.Two of the earliest marine phages genomically characterized were the podoviruses roseophage SIO1 (7) and vibriophage VpV262 (8). These exemplify a group of podoviruses that are vaguely similar to enterobacterial phage T7 but lack the singlechain RNA polymerase and have two converging transcription units rather than one unidirectional transcription unit. It was postulated that this description represented an ancestral phage type present in ancient oceans and widespread descendants would be found in oceanic bacterial species.Pseudoalteromonas is a genus of gammaproteobacteria with many species, all found in marine environments. The genus contains specialists for various marine habitats ranging from sea ice (9) to deep-sea sediments (10). Its species are divided into pigmented and nonpigmented species; the former are known for habitation of marine biofilms and p...

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“…SM9913 (GenBank accession no. ADT69962) (26). b All reactions were carried out at both 30°C and 60°C, and activities with the highest values are shown.…”

Section: Discussionmentioning

confidence: 99%

“…SM9913 (PsEst) (GenBank accession no. ADT69962) (26), which showed 56% to 66% identity with respect to Est22, were chosen for a study of their substrate specificities. The results showed that all three Est22 homologs could efficiently hydrolyze short-chain pNP esters (C 2 to C 6 ) and had no detectable transacetylase activity (Table 3), just as in the case of Est22.…”

Section: Discussionmentioning

confidence: 99%

A Novel Subfamily Esterase with a Homoserine Transacetylase-like Fold but No Transferase Activity

Yao

Wang

et al. 2017

Appl Environ Microbiol

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Microbial esterases play important roles in deep-sea organic carbon degradation and cycling. Although they have similar catalytic triads and oxyanion holes, esterases are hydrolases and homoserine transacetylases (HTAs) are transferases. Because two HTA homologs were identified as acetyl esterases, the HTA family was recently divided into the bona fide acetyltransferase subfamily and the acetyl esterase subfamily. Here, we identified and characterized a novel HTA-like esterase, Est22, from a deep-sea sedimentary metagenomic library. Est22 could efficiently hydrolyze esters with acyl lengths of up to six carbon atoms but had no transacetylase activity, which is different from HTAs and HTA-like acetyl esterases. Phylogenetic analysis also showed that Est22 and its homologs form a separate branch of the HTA family. We solved the structures of Est22 and its L374D mutant and modeled the structure of the L374D mutant with p-nitrophenyl butyrate. Based on structural, mutational, and biochemical analyses, Phe 71 and Met 176 in the oxyanion hole and Arg 294 were revealed to be the key substrate-binding residues. A detailed structural comparison indicated that differences in their catalytic tunnels lead to the different substrate specificities of Est22 and the other two HTA subfamilies. Biochemical and sequence analyses suggested that Est22 homologs may have the same substrate recognition and catalysis mechanisms as Est22. Due to the significant differences in sequences, structures, and substrate specificities between Est22 (and its homologs) and the other two HTA subfamilies, we suggest that Est22 and its homologs represent a new subfamily in the HTA family.IMPORTANCE Microbial esterases play important roles in the turnover of organic carbon in the deep sea. Esterases and HTAs represent two groups of ␣/␤ hydrolases. Esterases catalyze the hydrolysis of simple esters and are widely used in the pharmaceutical and agrochemical industries, while HTAs catalyze the transfer of an acetyl group from acetyl-coenzyme A (CoA) to homoserine and are essential for microbial growth. Here, we report on a novel HTA-like esterase, Est22, from a deep-sea sediment. Because of the significant differences in sequences, structures, and substrate specificities of HTAs and HTA-like acetyl esterases, Est22 and its homologs represent a new subfamily in the HTA family. This study offers new knowledge regarding marine esterases.

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Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913

Cited by 112 publications

References 63 publications

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

Morphology, Physiological Characteristics, and Complete Sequence of Marine Bacteriophage ϕRIO-1 Infecting Pseudoalteromonas marina

A Novel Subfamily Esterase with a Homoserine Transacetylase-like Fold but No Transferase Activity

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