Genome of the Haloarchaeon Natronomonas moolapensis, a Neutrophilic Member of a Previously Haloalkaliphilic Genus

Dyall‐Smith, Mike; Pfeiffer, Friedhelm; Oberwinkler, Tanja; Klee, Kathrin; Rampp, Markus; Palm, Peter; Gross, Karin; Schuster, Stephan C.; Oesterhelt, Dieter

doi:10.1128/genomea.00095-13

Cited by 10 publications

(5 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For the chromosome, we adopted the convention of choosing a position close to a canonical replication origin. However, we used a biologically relevant variation that we have used previously for Natronomonas moolapensis (Dyall‐Smith et al, ) and Halobacterium hubeiense (Jaakkola et al, ). Most haloarchaeal genomes contain a canonical replication origin that is flanked on one side by a distinctive, highly conserved paralog of the Orc/Cdc6 family, and on the other side by a highly conserved but divergently transcribed three‐gene cluster ( oapABC ; oap: origin‐associated protein).…”

Section: Resultsmentioning

confidence: 99%

Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754^T) and the laboratory strains R1 and NRC‐1

et al. 2019

Self Cite

View full text Add to dashboard Cite

Halobacterium salinarum is an extremely halophilic archaeon that is widely distributed in hypersaline environments and was originally isolated as a spoilage organism of salted fish and hides. The type strain 91-R6 (DSM 3754 T ) has seldom been studied and its genome sequence has only recently been determined by our group. The exact relationship between the type strain and two widely used model strains, NRC-1 and R1, has not been described before. The genome of Hbt. salinarum strain 91-R6 consists of a chromosome (2.17 Mb) and two large plasmids (148 and 102 kb, with 39,230 bp being duplicated). Cytosine residues are methylated ( m4 C) within CTAG motifs. The genomes of type and laboratory strains are closely related, their chromosomes sharing average nucleotide identity (ANIb) values of 98% and in silico DNA-DNA hybridization (DDH) values of 95%. The chromosomes are completely colinear, do not show genome rearrangement, and matching segments show <1% sequence difference. Among the strain-specific sequences are three large chromosomal replacement regions (>10 kb). The well-studied AT-rich island (61 kb) of the laboratory strains is replaced by a distinct AT-rich sequence (47 kb) in 91-R6. Another large replacement (91-R6: 78 kb, R1: 44 kb) codes for distinct homologs of proteins involved in motility and N-glycosylation. Most (107 kb) of plasmid pHSAL1 (91-R6) is very closely related to part of plasmid pHS3 (R1) and codes for essential genes (e.g. arginine-tRNA ligase and the pyrimidine biosynthesis enzyme aspartate carbamoyltransferase). Part of pHS3 (42.5 kb total) is closely related to the largest strain-specific sequence (164 kb)in the type strain chromosome. Genome sequencing unraveled the close relationship between the Hbt. salinarum type strain and two well-studied laboratory strains at the DNA and protein levels. Although an independent isolate, the type strain shows a remarkably low evolutionary difference to the laboratory strains. K E Y W O R D Scomparative genomics, genomic variability, haloarchaea, halobacteria, megaplasmid, type strain 2 of 44 | PFEIFFER Et al.

show abstract

Section: Resultsmentioning

confidence: 99%

Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754^T) and the laboratory strains R1 and NRC‐1

et al. 2019

Self Cite

View full text Add to dashboard Cite

show abstract

“…These genes point away from the origin, a configuration that is found in all haloarchaea. The chromosome ring was opened C‐terminal to oapC (Hhub_1001), as in the Natronomonas moolapensis genome (Dyall‐Smith et al ., ), to highlight the close association of the oapABC genes with the replication origin. Gene for an Orc1/Cdc6‐type DNA replication protein resided on the other side of the origin, pointing away from it.…”

Section: Resultsmentioning

confidence: 99%

The complete genome of a viable archaeum isolated from 123‐million‐year‐old rock salt

Jaakkola

Pfeiffer

Ravantti

et al. 2016

Environmental Microbiology

Self Cite

View full text Add to dashboard Cite

Live microbes have been isolated from rock salt up to Permian age. Only obligatory cellular functions can be performed in halite-buried cells. Consequently, their genomic sequences are likely to remain virtually unchanged. However, the available sequence information from these organisms is scarce and consists of mainly ribosomal 16S sequences. Here, live archaea were isolated from early Cretaceous (∼ 123 million years old) halite from the depth of 2000 m in Qianjiang Depression, Hubei Province, China. The sample was radiologically dated and subjected to rigorous surface sterilization before microbe isolation. The isolates represented a single novel species of Halobacterium, for which we suggest the name Halobacterium hubeiense, type strain Hbt. hubeiense JI20-1. The species was closely related to a Permian (225-280 million years old) isolate, Halobacterium noricense, originating from Alpine rock salt. This study is the first one to publish the complete genome of an organism originating from surface-sterilized ancient halite. In the future, genomic data from halite-buried microbes can become a key factor in understanding the mechanisms by which these organisms are able to survive in harsh conditions deep underground or possibly on other celestial bodies.

show abstract

“…For the chromosome, we adopted the convention of choosing a start position close to a canonical replication origin. However, we used a biologically relevant variation that we have used previously for Natronomonas moolapensis ( Dyall-Smith et al, 2013 ), Halobacterium hubeiense ( Jaakkola et al, 2016 ), and Halobacterium salinarum strain 91-R6 T ( Pfeiffer et al, 2019 , 2020 ). This point of ring opening highlights the strong syntenic association of the genes adjoining the major replication origin.…”

Section: Resultsmentioning

confidence: 99%

Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1

et al. 2021

Self Cite

View full text Add to dashboard Cite

Hypersaline environments are the source of many viruses infecting different species of halophilic euryarchaea. Information on infection mechanisms of archaeal viruses is scarce, due to the lack of genetically accessible virus–host models. Recently, a new archaeal siphovirus, Haloferax tailed virus 1 (HFTV1), was isolated together with its host belonging to the genus Haloferax, but it is not infectious on the widely used model euryarcheon Haloferax volcanii. To gain more insight into the biology of HFTV1 host strain LR2-5, we studied characteristics that might play a role in its virus susceptibility: growth-dependent motility, surface layer, filamentous surface structures, and cell shape. Its genome sequence showed that LR2-5 is a new strain of Haloferax gibbonsii. LR2-5 lacks obvious viral defense systems, such as CRISPR-Cas, and the composition of its cell surface is different from Hfx. volcanii, which might explain the different viral host range. This work provides first deep insights into the relationship between the host of halovirus HFTV1 and other members of the genus Haloferax. Given the close relationship to the genetically accessible Hfx. volcanii, LR2-5 has high potential as a new model for virus–host studies in euryarchaea.

show abstract

Genome of the Haloarchaeon Natronomonas moolapensis, a Neutrophilic Member of a Previously Haloalkaliphilic Genus

Cited by 10 publications

References 9 publications

Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754^T) and the laboratory strains R1 and NRC‐1

Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754^T) and the laboratory strains R1 and NRC‐1

The complete genome of a viable archaeum isolated from 123‐million‐year‐old rock salt

Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1

Contact Info

Product

Resources

About

Genome of the Haloarchaeon Natronomonas moolapensis, a Neutrophilic Member of a Previously Haloalkaliphilic Genus

Cited by 10 publications

References 9 publications

Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754T) and the laboratory strains R1 and NRC‐1

Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754T) and the laboratory strains R1 and NRC‐1

The complete genome of a viable archaeum isolated from 123‐million‐year‐old rock salt

Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1

Contact Info

Product

Resources

About

Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754^T) and the laboratory strains R1 and NRC‐1

Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754^T) and the laboratory strains R1 and NRC‐1